If the PDF files were added directly to iBooks on the iPad, then they probably did not sync back to iTunes. It's a known issue. They only sync properly when added to iTunes first.
What this means is that your PDFs are gone, unless you have them backed up elsewhere. Sorry.
Like any computer, only more so with mobile, it is a really bad idea to keep important documents stored in only one location and device. Old techs like me have learned this the hard way; usually right after the third or forth incident and all night recovery effort that ends up taking all week.
If you don't have a computer to keep copies on, I recommend a cloud service like DropBox or Box.net.
Hopefully you can find all the PDF's you need again.