I have my PDF's on my iPad but I do not see them on my iPhone? How do you back the PDF's if you have hundreds on the iBook? I know you have one by one email them to yourself but that will take a long time.
iPad Air, iOS 9.2.1, null
PDFs and/or non-bookstore books aren't stored in the cloud. Try connecting the iPad to your computer's iTunes and do File > Devices > Transfer Purchases to copy them over to your computer (that should copy PDFs/epubs in the iBooks app, not just ibooks), and if using a Mac with iBooks on it then do File > Move Books From iTunes in it, and you can then sync them to your phone and take a backup copy of them
The synced collections doesn't seem to work for non iBook store purchases.
