Sync iOS iBooks to OS X iBooks
I have a similar problem. Non-iBook store epubs don't sync with iOS devices, no matter what options are switched on/off.

Looking at the directory they're now stored on in Mavericks (~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks/Books), they seem to have been converted to a different format (from .epub to a folder with xml/html files), and i suspect that's why they don't sync.

Any suggestions on how to sync these would be most appreciated!

EDIT: To answer my own question, check that iTunes is actually syncing all books. It had changed my previous preference to selected books, and preferentially un-ticked all non-iBook store epubs. Changing that fixed the syncing problem for me...