IOS – EPUB files are not syncing through iCloud for iBooks along with iOS 9.3

I finally got this working by signing out and signing in again in the iBookstore. It then asked me if I wanted to sync, I said yes, but it still didn't work, so I went to Settings and saw that the sync switches were off, and now it works. Phew!

You might have the wrong idea (in Apple's eyes) about syncing through iBooks. You will not be able to have content magically appear on your second Mac, if the book is not purchased through the iBooks Store. Syncing does not work iTunes Match-like.

For non-iBookstore files, like MobileRead epubs, you will need to transfer the same epubs you imported onto iBooks on machine 1 to machine 2 and import them again. I hope you still have copies of these files -- because as far as I can tell, iBooks splits up epubs you import into it, and you cannot get them back out as an epub again. (I would love to be wrong about this.)

The good news is: Once you have imported these files, syncing between Macs works for notes, reading positions and highlights, as long as you have enabled "Sync bookmarks, highlights and notes across devices" in iBooks preferences. Again: iBooks will only sync said bookmarks, highlights and notes, NOT the books themselves. You will also need to have logged in with the same Apple ID on both devices.

Needless to say, you should also make sure to run the latest version of iBooks (currently 1.0.1).

This might be the only advantage of (and reason for) not being able to change metadata in iBooks -- at least the software knows which files are identical...