IBooks disappeared after upgrading to iOS6

I had about 25 PDF's in iBooks and all but 2 disappeared after updating to iOS6, where should I look for them?

Hello, unfortunately I can't find where my iTunes stored the back-up. In the article the path which is described -
Windows Vista, Windows 7, and Windows 8: \Users\(username)\AppData\Roaming\Apple Computer\MobileSync\Backup\, doesn't exist. In the folder /Program Files/Itunes/ doesn't exist a folder backup or something similar. I forgot to mention that my device is an Ipad and the pdf. files are all collected from different sites, none of them is purchased.

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