Yes, I know. I definitely didn't ask for it, so something out of my control/knowledge purged what I had in iBooks (talking to Apple they more or less admitted it was something on their side of things and said nothing could be done in this case).
I searched the web for ”ibooks pds disappear” and found several cases where people had experienced the same thing. Several suggested fixes and I think I've tried them all now and decided to just start over – luckily none of the PDFs I had is irreplaceable, so what I have lost is simply the time I spent on finding them since I had removed them from everywhere else than iBooks. But it's PDFs I've found online (product manual and LEGO instuctions etc.) and some for my studies which is possible to obtain again. Still sad to have spent time on thing that has to be done again, but I would of course be much worse if I lost things that couldn't be brought back.
I'm now trying to inform people about that what they have added to iBooks isn't really backup by normal means, so it's a good idea to copy the PDFs there out of iBooks too to make sure there aren't only residing in the cloud. I really think those PDFs should get backed up at least when doing an iOS backup onto iCloud.