I had a similar problem after downloading a library book. I had multiple copies of some of my books that wouldn't delete, and they didn't show up in the desktop app or ADE. Plus, I couldn't open any of the books I'd side-loaded with ADE. Things were pretty messed up.
I had to do a factory reset to get rid of the extra books and then reload all my books onto the device. It works fine now (but I'm kind of leery of library books)...