I know this is an old thread, but I have to say thank you for this post. I had a corrupt file on my reader and couldn't figure out what had happened. So I did this . . .
If that doesn't work, or you can't remember the books, you should remove all the books that the Kobo doesn't have in it's library (delete them while connected via USB), and then add them a few at a time until you find the one that was bad.
And that solved the problem.