There seems to be a real dropping of the ball by Apple on backing up and syncing up iBooks contents, particularly PDFs and other things not purchased from the iBooks store. I made the mistake of thinking that a full backup to iTunes of my wife's iPad would sync all of these and we lost several PDF books she had downloaded. I'm about to update to a new iPad myself and don't want to suffer the same fate. Problem is, nothing seems to be working. I try to "Transfer purchases from iPad" in iTunes and nothing happens. I try to sync all the iBooks stuff in iCloud using iBooks for Mac, and it leaves out some PDFs. I can transfer them one by one through email but it should't be this hard. Does anyone have a 'no fail', works every time method to getting all your iBooks stuff synced so that it can be restored on a new device?