Getting error 82 when transferring my website over SSH

I'm trying to upload my website to a Linode server and only some files are able to go through; most others give an error 82. This is one of those cases where every single file must be left intact during the transfer process. I can't even upload a .zip containing everything to unzip once its there. Dopus thinks the directories don't exist even though they clearly do on my local machine thus I'm trying to copy them over to the server. I can't delete the folders with the missing files that Dopus won't copy over for this same reason, thus I'm forced to rm -r my site's root directory in OpenSSH to do it, which is a real shame because I was drawn to this file manager for its FTP/SSH integrations.

This was what was captured from the logs (my directory uses my domain name which I'm omitting here for privacy reasons):

SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Media/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Media/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Markdown: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page/Medium: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Page: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors/Events: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Processors: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Scheduler: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Scheduler: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Scheduler: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Scheduler: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Service: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/Node: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig/TokenParser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/Twig: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/DataUser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/DataUser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/FlexUser/Storage: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/FlexUser/Storage: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/FlexUser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/FlexUser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/FlexUser: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common/User: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Common: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Cli: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/Gpm: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Console/TerminalObjects: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Adapter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Adapter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Adapter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Adapter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Adapter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Cache/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/ContentBlock: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/ContentBlock: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/ContentBlock: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/ContentBlock: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/DI: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Formatter: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/File: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Filesystem: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Filesystem/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Storage: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Storage: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Storage: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Storage: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Flex/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Form: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Form: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Form/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Form/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Form/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Form/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Media/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Media/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Media/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Media/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Access: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Access: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Access: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Access: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Access: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Base: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Base: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Collection: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Property: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Property: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Property: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object/Property: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Object: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Pagination: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Pagination: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Pagination/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Pagination/Interfaces: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Pagination: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Pagination: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Parsedown: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Parsedown: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Psr7: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Exception: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Middlewares: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/RequestHandler/Traits: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Route: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Route: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Session/Exceptions: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Session: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Session: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Uri: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Uri: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Framework/Uri: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/src/Grav/Installer: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/templates/partials: no such file or directory
SSH: Directory /var/www/html/[DOMAIN NAME]/public_html/system/templates/partials: no such file or directory
SSH: rm /var/www/html/[DOMAIN NAME]/public_html/system/aliases.php: OK
SSH: Listing Directory
SSH: List complete 3 files.
SSH: Listing Directory
SSH: Unable to open .: no such file or directory
SSH: /var/www/html/[DOMAIN NAME]/public_html/www.zip: no such file or directory

I'm posting this since the existing topics about this issue are outdated. Hope to hear back soon

Are the paths in the error messages ones which look correct and do exist?

Have you tried using another SFTP client to do the same copy (same file and destination)?

Alright I woke up this morning and tried copying over the same folder containing the files from the logs last night and strangely I didn't get those errors this time & everything in it managed to go through. I don't know why it would throw up errors last night but then some hours later it suddenly goes through fine?

I'll try transferring the rest of the files over hoping it all goes well with those too. Since you asked about whether or not the paths 'looked correct' how would I know whether or not it does? How can I check if it does? What other measures should I take to ensure no more errors happen when transfering files over (S)FTP?

Are the paths an exact match for the ones you were using elsewhere? e.g. in your SSH window. In other SFTP clients.