Epubs from iBooks not showing up in iTunes on Mac OS X Sierra
OK, I’ve managed to solve this with the help of another guy from Apple Suport Forum.

Here’s what I did:


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


Here’s the original forum post.