Use these steps to update iBooks and migrate your remaining books.
- Begin by updating to iBooks 1.0.1. You can install this update from the Updates tab of the Mac App Store, or by choosing Software Update from the Apple menu ().
- Once iBooks has been updated to iBooks 1.0.1 re-migrate your books by selecting File > Move books from iTunes.
This moves any additional PDFs or books from iTunes that weren't previously migrated.