Is it possible to sync the contents of ibooks between devices when the books have not been purchased from itunes?

Even if they aren't iTunes purchases, as they are in the iBooks app you should be able to copy them over to the Books part of your computer's iTunes library (they will go into the iBooks app if you are using a Mac with OS X Mavericks on it) via File > Devices > Transfer Purchases and you can then sync them to your other device(s)