PDFs fail to load from backup

I upgraded my iOS recently. In the process, I took a backup of my iPad 2. In addition to some purchased books, my iBooks had a lot of other books that I downloaded from the net, a lot of them marked with some important info I can ill afford to lose.
When I restored from the backup, only the purchased books were restored, and the rest lost. How do they restore the other books, and the associated notes/highlights/comments ?
Also, I was unable to restore the images from the backup.
Please, please help me.

Thanks Meg :)
I called the service centre up, and they asked me to do the same too. One pointer though for someone facing the same problem - if you lay your hands on the link from which you downloaded the original PDF/ePub, any notes/comments/highlights in the book will be retained

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