@Pilgrimpez You’re probably not doing anything wrong and it’s likely that this issue is related to this and this one, where I see you left a comment.
Kindly send your logs.db and out.txt files to support@insynchq.com with the link to this post, and include a few names of files or folders that were deleted.
To collect your logs, quit Insync first then go to ~/.config/Insync afterwards to find the requested files. We’ll investigate this and will let you know what steps to take next.