iTunes loses track of books in iBooks when syncing

This is an ongoing issue. Last time I synced with my iPad iTunes put 2200 files on my iPad. Today I plug the iPad into my Mac Pro and I see 1742 books. If I were to sync it would remove about 500 files from my iPad instead of putting on the 20 that I added to iBooks. I've submitted feedback on iTunes I've submitted feedback on iBooks and gotten no help at all. Short of blowing everything away and reloading all those files is anybody have any suggestions? Or am I the only person in the world having this problem?