I assume that you are talking about PDF files in the iBooks app. If you restored from the iTunes backup and the PDF files were not restored to the device, try syncing them from iTunes. Connect the iPad to the computer, launch iTunes, select your iPad under the devices heading, click on the books tab in iTunes, then make sure that all of the PDF files have been selected to sync, then sync.
If you make changes to the sync Settings, the sync button will turn into Apply. Click on that to apply the changes and sync the files.