You can redownload them, but that's about all other than resyncing. Are you running on the iOS 5 beta?
From Apple's site:
Can I download my previously purchased book again at no additional cost?
Yes, you may download past purchases from the iBookstore at no additional cost. To download a book again, tap Store, then tap Purchased. Find the book you want to download again and tap the download button. You must be logged in to the iBookstore on your iOS device or iTunes Store on your computer using the Apple ID you originally used to purchase a book in order to download it again. View this article for more information about downloading past book purchases directly to your computer. Previous purchases may be unavailable if they are no longer on the iBookstore. Downloading previous purchases is not compatible with iPhone 4 (CDMA Model).