Devices in use: 2011 iMac running macOS Sierra and iTunes 184.108.40.206, iPad 3 (Retina) running iOS 6.
It's been a month or two since I have needed to sync any books to my iPad, but today when I went to do so, iTunes has unchecked the Sync Books option somehow. I did not do this. All the books are still on my iPad, and are also in iBooks on the Mac. But if I tick the Sync Books box I am prompted that all content on the iPad will be replaced, etc.
Also, iTunes only shows 12 of my 73 books. But if I go into iBooks and select Move Books From iTunes (which actually does the opposite, move books from iBook TO iTunes), then they all appear in iTunes. Then however if I select Books from "On My Device" in iTunes, and then go back to Books from "Settings", I'm back to the 12 books again in iTunes.
Am I crazy or does "Sync" not actually sync? To me Sync implies 2-way synchronization of information, but it seems that if I tick the Sync Books box in iTunes and Sync, I will get a 1-way push of data from the iMac that will overwrite the iPad and cause me to lose all the books already stored there.
How can I get iTunes to enable sync again without blowing out all the content on my iPad? I have it all in iBooks as well but I have many highlights and such on the iPad, and I'm afraid of losing them all if I just re-sync to the content in iBooks.