ICloud – Locating the iBooks folder in iCloud Drive

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...

I finally managed it by re-creating my iTunes library as mentioned here: http://support.apple.com/kb/ht1451.

After moving the .itl file I also moved the Books folder under iTunes Music.

It takes quite some time to import, depending on the size of the library, and it will finally warn that some items could not be found - which is obvious after deleting Books.

After that the contents of iBooks appeared in the Books sync tab.

Edit: Unfortunately, all my apps for my i-devices were gone, too. I had to manually transmit them device by device via the menu item File>Devices>Transfer Purchases from (device name). This step is clearing all the apps that I haven't synched to any of the devices at this time, which might be good or bad. However, I can download them again if I'm in the need for that.