IPhone – Specfic epubs downloaded outside the iBooks store not syncing on a particular mac

I have a handful of epubs I downloaded outside of the iBooks Store and read them across two different macs and an iPhone.

For reasons I cannot explain some books’ data (highlights, notes, place in book) will sync across the devices while others do not.

The following options are turned on in my iPhone settings:

• Sync Bookmarks and Notes
• Sync Collections

On both macs I have the following turned on:

• Sync bookmarks, highlights, collections across devices

I have not used syncing via iTunes. So some books sync via iCloud while others do not.

Despite syncing turned on, I cannot get a Macbook Pro to sync with the highlights on the iPhone for certain book. I drag the epub into iBooks on the Macbook and it thinks its a “new” book. FWIW, I have a Mac Mini that seems to sync fine.

How can I correct this?

Hardware:

Macbook Pro
Intel Core i7 3.1 Ghz
OS X 10.11.4

Mac Mini
2.3 GHz quad-core Intel Core i7
OS X 10.11.4

iPhone SE 64GB
iOS 9.3.1

Thanks in advance.