Yesterday While trying to sync all my ePubs and PDFs from Mavericks iBooks to my iPad it wasn’t working.
All the Books and PDFs I had in iTunes prior to upgrading have worked fine but since then none of the new ones did.
Here is the fix
While in iBooks for Mac, Click on File and Select Move Books from iTunes
At that point, You should see this
Once that completes, you will get the following Message
That’s it, if you now plug your iPad into iTunes, The books section will show all those missing books and PDFs