Some of my books are disappearing from ibooks. Help?

Okay, so most of my books are not from iBooks, but I've never had an issue with it before the last couple of days. Now for some reason the newest dozen or so books I've added disappear after I close iBooks (but a couple of yesterday's newly added books have stayed in ibooks). I re-add them and when I've finished browsing I close it, open it again to see if it's happened again and it has. They're gone. BUT, when I go to re-add them it says they're already in my library, but if I do a search none of them come up.

I managed to sync those books to my iPad Mini and they're still on that, but not in the desktop app. Why has this started to happen all of a sudden? I've been remarkably free of El Capitan issues so far. I haven't touched any of the settings, nearly all of my other books are there.