iBooks is deleting my books

I have a lot of EPUB and PDF books that I've gotten elsewhere over the years and loaded into iBooks on my iPad. (For example, by syncing through iTunes in the old days, or by syncing through DropBox or downloading in Safari and doing an Open in iBooks.)

Since iOS9 (I think) they've been vanishing. At this point, I think all my manually loaded books are gone. Some had been there for years.

What's going on?