I'm having the same problem transfering iBooks that I downloaded from the Apple Store. When I check the iBooks Sync in iTunes on my PC, a warning pops up saying that if I continue all music, movies, and TV showes will be removed from my iPad.
I continued with the sync and a copy of the iBooks on my iPad were transferred to iTunes on my PC, but it Did Remove all my music, movies, and TV shows from my iPad.
Is this a bug or am I doing something wrong? I might add that I manual sync music, movies, and TV shows to my iPad and Touch.
Ok, try this, it worked for me. Right-click on your iPad/iPhone/iPod Touch in the sidebar. Click "Transfer Purchases." When it is finished, go to the iTunes Preferences (Command+, on a Mac and Ctrl+, on Windows) and enable Books. You should now have a Books tab in your Library and your books should all be there. Hope this helps!