Epubs from iBooks not showing up in iTunes on Mac OS X Sierra

Solution 1:

OK, I’ve managed to solve this with the help of another guy from Apple Suport Forum.

Here’s what I did:

1. I Quit the iTunes
2. I opened iBooks
3. I backed up my books and PDF’s from iBooks by dragging and holding alt copying them to a backup folder
4. I deleted all of my books and PDF’s from iBooks
5. I quit the iBooks
6. I went to the Settings > iCloud > Options > iBooks and turned the iCloud support for iBooks off
7. I went to the Library folder in Finder and located the nsurlsessiond folder via search
8. I copied the folder to the backup folder, just in case
9. I deleted the nsurlsessiond folder
10. I shut the OS X down
11. I turned the computer on
12. I opened iBooks I moved my books and PDF’s from the backup folder to iBooks
13. I turned the iCloud support for iBooks on (see the step 6)
14. I opened iTunes
15. Voilah! All of my books and PDF’s are there!
16. I synced the books successfully to both iPad 3 and iPhone 6
17. I checked the highlights, bookmarks, notes and the last page read and everything was properly syncing

Here’s the original forum post.