Yeah the books were in ".kobo/kepub" directory and I too couldn't really understand why they weren't showing up on the kobo either. I have since copied a bunch of ebooks across (no kepubs though) and all is working well.
I'm happy to send you any files - just point me in the direction. I still have a copy of the .kobo folder from before I deleted the books if that helps. I had copied it before I dared delete anything from inside the folders.