iBooks sync

I have a MacBook Air and iPad mini running 12.1.2.27 and iOS 8.3 and are having trouble syncing my full iBooks library on Mac to my iPad, libray has 4900 books and I have selected the sync all books check box in iTunes but the sync keeps self cancelling and only half the books stay on the seem tomstay on the mini. I have 100 GB free in iPad. The books are a mix of iBooks purchases and ePub downloaded in to ibooks