iBooks and iTunes not syncing
MacBook Pro, OS X El Capitan (10.11.5)
And I have started having a similar issue with synching audiobooks that are on my PC with my iPhone. This seems recently to have gotten much worse. In the past an occasional restart of the iPhone, the PC, or both (maybe once every couple months) has now become a struggle to get anything to sync easily.
The iBooks/iTunes/iCloud family is a great idea... it's a pity it doesn't work properly! However, I've observed that issues with the 'iFamily' often follow OS (sometimes iOS) updates and upgrades. What has worked for me is to perform a safe boot on my Mac (hold the shift key on restart/start up). Then go to System Prefs./iCloud and sign in and set up. If necessary, sign out and in again. Do the same for your iBooks and iTunes accounts. Then restart as normal.
As I say, it's worked for me on several occasions when books were not syncing with iTunes or iCloud Drive.
iBooks and iTunes not syncing