1) Backup your iPad to iCloud
— Turn on iCloud Backup if it is not already on.
— Under “Backup Options” deselect iBooks (make sure everything else is selected)
— Delete the iBook App
— Tap “Backup Now” and wait for the back up to complete.
2) Reset your iPad
— make note of your AppleID and Password in iCloud
— turn off “Find My iPad”
— goto Settings–>General–>Reset
— choose “Erase All Content and Settings”
3) When the iPad starts, choose “Restore From iCloud Backup”
4) Reinstall iBooks
5) Download your iBooks from “Purchased Books” collection.
Some people have also used IIRC via iTunes but that didn’t work for me.
Hope this helps.