Apple - 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...

You absolutely can sync notes and highlights for ePubs not purchased from iTunes when using iBooks on your Mac and iOS devices.

Here is how:

1. Place your not-purchased ePubs in iBooks on your Mac.
2. Connect your iOS device to your Mac.
3. Open iTunes.
4. Select your iOS device in the left column.
5. Click Books.
6. Choose All Books or Selected Books.
7. Click Apply to copy the books to your iOS device.
8. Repeat steps 2 to 7 for other iOS devices.
9. Enable notes and highlights syncing for iBooks on your Mac and each iOS device.
10. Make notes and highlights in any of the ePubs you have copied from iBooks on your Mac to your iOS devices. These notes and highlights sync to all other devices.

It is very important to use the same version of the book on you Mac and all of your iOS devices. You cannot download an ePub from Gutenberg to your Mac and then download it again to your iOS device and expect notes and highlights to sync. That probably won't happen. If you think it through, this makes sense because iBooks needs to know for sure which files to use for syncing and file name alone is too imprecise.