I am using iPad 2. After upgrading to the new iOS 9.1, the PDF is missing from iBooks. This is really weird. I am not sure this is one of iOS 9 new features.
Look at the following two simple questions to get your iPad seen PDF again.
- Have you manually synced the PDF files to your iPad using iTunes?
- Do PDF files appear in the case you select the PDFs to sync them?
The first question should figure your problem out.