Unless I am mistaken, PDF files are not backed up, i.e. they simply remain on your computer.
I cannot understand why they were not restored.
Did you move those PDF files to another directory on your computer?
Connect your iPad to iTunes on your computer, then have a look in Books to see whether your PDF files are there.
If they are, you may merely have to sync your iPad.
Look out for any error messages.
Alas, with the iPad plugged in and iTunes running, iBook PDFs are empty. I checked the help site
and under the heading 'what does iTunes back up,' it clearly states:
Application settings, preferences, and data, including documents.
So..., where might the PDFs go?