It sounds like you didn't do a backup of the old iPhone followed by a restore of that one to the new iPhone. If you do the backup/restore thing you shouldn't lose information from apps. I don't use iBooks, and thus don't know how it handles highlights, but I think Amazon does it by creating a companion file for the highlights, notes, etc. If you don't have sync turned ON then Amazon cannot sync that file to its cloud. I'm guessing iBooks is similar. So make sure you have sync turned on for any reading app to ensure highlights, notes, etc. get backed up to a cloud somewhere.