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Helpful answers
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Jul 15, 2016 2:12 PM in response to CESNETby Carolyn Samit,Make sure your iPad software is up to date.
Tap Settings > General > Software Update
Latest iOS version for iPad is 9.3.2
Also, in iTunes on your Mac. If your Mac is running v10.11.2 as your profile suggest, you need to update OS X.
Open System Preferences > App Store then click Check Now. Latest version for El Capitan is v10.11.5.
Keeping your iPad and Mac software up to date can help with syncing your iBooks.
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Aug 18, 2016 5:29 AM in response to CESNETby G Michael Otto,Same problem. Also seen it on another user's Mac/iPad where only some of the books in iBooks library show up in iTunes when attempting to sync. There has got to be a bug somewhere that Apple hasn't found in the last year of nagging them.
I went through the pain and torture of finding the books on the cloud and copying them to the computer, deleting all the plists associated with iBooks and rebuilding the library (I have close to 2,000 books and pdfs in the library). Everything worked just fine....for a while....now yesterday I added 14 pdfs to the library and iTunes sees none of them. I renamed one of the collections and created a new collection for the 14 new pdfs and neither the renamed collection nor the new collection show in iTunes nor did they sync when I told iTunes to sync the entire library.....I suspect that some books were actually removed from the iPad since iTunes has lost track of some of the books it previously saw. This is really frustrating since I do NOT want to use the books in the cloud since they have to be manually downloaded to the iPad or iPhone and with so many books I'd spend all my time clicking on that cloud button and never reading anything.
The answer from Apple support was to use iCloud, yada, yada, yada because that's the way it is designed to be used which strikes me as either arrogant or stupid. And after struggling for an hour with a friend yesterday who has the same problem and is using iCloud...same symptoms..some books showing and some not I don't see any difference.
Has anyone figured this out yet?