I had the same issue. I upgraded my iPad 2 (old!) to iOS 9.3. At some point a few days ago, it asked me if I wanted to sync iBooks through iCloud, or some such. Thinking this was a good thing, I said yes, and discovered yesterday that all of my PDFs had vanished off of my iPad. Luckily, they were still on my Mac when I opened the iBooks app on there.
But, I couldn't figure out how to export PDFs out of iBooks on my Mac en masse, so here's what I did to get them back onto my iPad:
- Using the search box in Finder, I looked for all PDF files on my Mac. I discovered the files were in a folder called iBooks on my iCloud drive.
- I looked in my iCloud drive folder, but there was no folder visible called iBooks.
- I went to this site to figure out how to show hidden files, but when I looked the iBooks folder still wasn't visible in my iCloud drive
- So, again searched for PDFs across my whole Mac using the search bar in finder. Control-Clicking on one of my PDFs, I chose to "Open containing folder"
- In the containing folder (iBooks - but hidden and inaccessible), I copied all of the files in there. (And promptly backed them up to Dropbox.)
- Then, I pasted all of those files into a brand new folder I created and named iBooks on my iCloud drive, thinking that perhaps it would replace the hidden an inaccessible folder somehow.
This worked! When I went to my iPad, it again asked me if I wanted to use iBooks for iCloud. Figuring I had nothing to lose at this point, I said yes again, and all of my PDFs reappeared in iBooks on my mac after it seemed to do some kind of syncing over the air. When they reappeared, they were all sorted the way I had them originally, so I seemed to be no worse off than before. (I then went back into Terminal and did the commands to hide the hidden folders again.)
My only guess is that the iBooks / iCloud syncing doesn't work well with older hardware - the iPad 2 in my case - even though it's still being supported through iOS upgrades.
Moral of the story after 2 hours of work? I've learned the hard way to not have critical files synced only through Apple-based syncing systems, since so much buggy stuff happens behind-the-scenes, ostensibly to make things easier.