I was using Insync on a symlink folder. It synced everything to Google Drive. But when I used a different sync tool to sync that folder to another HDD it showed to new, empty folders somewhere inside of my folder. They had the names of already existing folders, but with " (2)" at the end of their name. I don’t know, what caused the issue and whether it is related to the symlink or not (just started to use Insync). Hope this can get fixed.
I will send the logs when I am on that computer again.
Just sent them to you.