I didn't have to back up any of my voice recordings before upgrading to IOS5 (eg, in my SoundNote app) and they are all still there. But my PDFs -- except two -- are gone. Why didn't those two disappear, I wonder? I opened and saved them like all the others.
Apple has stuffed up here, no question.
I had the same problem when I upgraded my iOS from iOS4 to iOS6. The ipad setting showed that there was some data and documents in iBook, but I found only an empty shelf in iBook. When I connected to the latest version iTune, it showed that my iPad did not have any PDF files. After reading many posts about the similar problem, none of suggestions worked out for me. However, I tried to connect my iPad to another computer with older version of iTune (no sync allowed) and found that all the PDF files were there in the iPad. Therefore, I could copy those files and backed it up in my computer. That is how I retrieved all my PDF files. Hopefully, it will work for you.
Originally Posted by grdn19