Sync'ing via iTunes and USB

I have a number of ebooks (mostly Take Control books) on my iPad. These have been annotated with notes and highlights. I was attempting to sync these annotations back to my Mac using iTunes v12.9.5.5 on Mojave. Instead, it deleted the books from my iPad. And the versions on the Mac do not contain the annotations.

I have tried to re’sync to get the books back on the iPad but no success.

It shouldn’t be this hard.


Edit: I am especially interested in saving the notes/annotations from these eBooks. Before the sync I did a backup using iTunes so maybe they exist in the backup. And one of the books was Take Control of iCloud so I could figure out if I wanted to do the cloud thing for syncing.

I sync all my books via icloud. Seamless. On Mojave/ipad iOs15

iMazing may well be able to pull individual eBooks from your backup.

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I had not considered that so I allowed iMazing to view the iTunes backup. Alas, there is no info for Books in the iTunes backup. If I dig deeper into Files there might be info – but that’s a tricky place to play.

I’m pretty certain that I will be able to push the ePub books back on the iPad – but it appears that all the annotations and notes may be lost. Curse you, iTunes.

Unless things have changed in the last couple of years, Apple stores the notes/highlighting for an epub in a database, not the book itself (I don’t know about pdfs). That way if you do sync, it usually only needs to send that, not the whole book. If you put a copy of a book back into Books, all of the notes should show up again. I don’t know how apple discriminates between similar books, but it doesn’t actually have to be the copy that was in Books to begin with and notated.

If you do get the notes back, it’s worthwhile backing up just the notes, though it’s somewhat tedious. For each book, go to the notes section, select them all, and share them. I use email though other options might suit you better. I don’t know of a way to apply them back into a copy of the book though.

I gave up on apple books years ago for several reasons, and now use Mapleread (all three flavors, CX, CE and SE). It will not only let you save a copy of the notes, but for email it includes an attachment so that you can glue them back into a copy of the book on another device without needing to sync. I really wish they’d make a Mac version–I have yet to find a good epub reader for the desktop.


I was finally able to restore the ePub books to my iPad – with notes and annotations.


By signing in to iTunes – even though none of the books was purchased through iTunes. They were purchased from Take Control. I use iTunes all the time – but rarely ever sign in.

That probably explains why I could not sync the books back to the iPad – and may also explain why they were removed from the iPad in the first place.

And, as you indicated in your reply, the notes showed up. Thanks!