Non-standard configurations don't imply that you're running stuff with paths hardcoded to folders on the HDD, though. If you want to do that then go for it but it's not relevant to this thread.
The root post is about editing things like the FTP config and seeing cahnges made to a USB version affect the HDD version's configuration. That should not happen unless the HDD version was still running (i.e. wasn't exited properly).