HI All,
I have same problem with iBook3. But I found solution to revert/restore iBook2. I already restored iBook2 and I can read all of my PDF.
Here is my solution for PC or Notebook users-
1) Please look for ibook 2.2 in your Recycle Bin (sorry I don't know how to find deleted items on Mac). I hope you didn't empty Recycle after updated iBook 3.0
2) If you find ibook 2.2, you are safe. please follow the following steps
3) remove iBook 3.0 from your iPad by Press iBook icon and click x mark to delete. Then just sync iPad with your PC or notebook.
4) Please go to "Music\iTunes\iTunes Media\Mobile Applications" on your PC or notebook and look for iBook 3.0 and delete it.
5) Please go to Recycle Bin and restore iBook 2.2 and ensure that iBook 2.2 is in "Music\iTunes\iTunes Media\Mobile Applications".
6) Restart iPad by pressing Power button and home key. (this step might not need but I did it)
7) After restarted, sync again iPad with PC.
8) Open iTunes and go to Library and look for Apps and then look for iBook icon and double click to lauch. It will prompt you to look for .ipa file. Then locate iBook 2.2 app at "Music\iTunes\iTunes Media\Mobile Applications" and click "Open".
9) Then Click your iPad under Device in iTunes and click Apps on the right pane. Then you will your iPad home screen.
10) Pleae tick Sync Apps and look for "iBooks".
11) Tick "iBooks" and click sync. you will see iBook 2.2 on your iPad after synced.
For me, I got all of my PDF back even if I deleted iBook 3.0
Hope this help.