I had the same issue - I opened ibooks on my ipad air 2 some days after upgrading to 9.3.1, and it asked if I wanted to sync using iCloud (don't know if it said icloud or icloud drive). I said yes, and immediately a large part of my pdf's disappeared.These were only present on my ipad. Also some books were gone.
Somehow I thought of going to settings - icloud - icloud drive and turned the toggle OFF for ibooks.
Now all missing pdf's and books are back again.
I'm afraid to sync with icloud drive again - I think they'll disappear again. So, basically, I can't use icloud drive with iBooks, because half of my content will be gone.
Edit: Tried it, turned the toggle back on: and now it's syncing properly.