All iBooks content lost after transfer to new iPad.

I recently purchased an iPad 2 and after moving all the contents from my old iPad I have lost everything in iBooks. There is the option to redownload one purchased one but all samples are lost. More importantly though all of my PDFs have disappeared.
I would assume that they are still somewhere in the last backup from my original iPad. Is there any way to retrieve them from the backup?

Open iBooks, tap Library if you happen to have a book open, otherwise tap Store (upper left corner). When the store app opens, tap Purchased (lower left). You should be able to redownload any books you previously purchased through iBook.

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