I simply set up a directory called "1" with two directories inside, "1" and "2", with 2 identical file, 1.txt and 2.txt. These two files are also outside of dir 1 and 2.
The target folder is empty.
Synchronize is file based (although filters can consider folders/paths when deciding which files to copy across etc.). I don't think it will delete folders in the destination that don't exist in the source; only files, if the corresponding option is on.
(Assuming that's the issue. Not sure if I'm paying attention to the right detail in the screenshots.)
But this worked in older version. I tested it with V11. In V13 there is written "Delete from destination, 1 File, 2 Folders" but the folder are not deleted. The folders counter is also wrong. These are 3 folders to be deleted.
I have the same problem. Files AND folders are no longer deleted in the destination. So you can no longer mirror the source with the destination. Orphaned files and folders remain in the destination that do not exist in the source. Even local, not only SFTP.