PDF's missing from iOS9 iBooks

I have the same problem all work related PDF files , certificates of learning ,billing statements plus numerous free crochet patterns accumulated over the years were saved to iBooks and I only noticed have gone missing - did you ever solve this ? I can see some on another device anxious to do anything in case they disappear too.My iBooks has duplicate but empty folders on the iPad2 I updated .Who can I ask for help ?

All my manually downloaded PDF's have been wiped off my iPad after syncing to iTunes on my new El Capitan OS. I opened up iBooks on the iPad, and I saw the 50-60 PDF books I had in there, and after 3 seconds, they all disappeared. Stunning feature Apple. They have been wiped out for no reason at all. I have sync with iCloud on, and they manual PDF's don't sync, only books from store which is useless for me.

I had had a similar problem occur on my iPad 3. I'm a prodigious reader. I have a LOT of PDFs and ebooks on my iPad.

After spending an hour sorting the PDFs in a folder this afternoon, iBooks froze. I tapped the home button which took me back to the home screen. I didn't double tap and shut iBooks down. On opening iBooks again, at least 40 PDFs had disappeared! They don't appear in a search, and iTunes shows them as no longer on the device. It appears I have no choice but to copy them back and rearrange them AGAIN! Every iOS update seems to be making my devices less and less stable. What's the point of paying premium Apple prices for hardware that can't be relied upon to retain data! I've got my books backing up to the cloud but can't find any way to restore them to my iPad from there.

I haven't permanently lost anything, but it's time consuming and inconvenient.

How do you contact the iBooks development team about problems like this?

I, too, have apparently lost all my PDFs from iBooks. I have two questions:

1) How do I get them back? I have tried to retrieve a backup but system indicates insufficient space to retrieve backup.

2) How has this deletion been allowed to happen?