I would have to say it threw them away, rather than lost them. It seemed a deliberate act.
I settled down this afternoon to continue reading on my iPad, opened iBooks, selected the book I was reading. The book opened up, displayed my page, and then iBooks dropped out. When I restarted it, all my loaded books were gone. The books from the iTunes store were there, but everything I had loaded from my own sources was gone.
Earlier this afternoon, I backed up my iPad to iTunes. I don't sync books. I didn't change any sync settings. I'm not sure if this is related, but from my reading, it appears it might be.
I used to use BlueFire reader, but with the iOS7 update, it got twitchy. If I tapped a book the wrong way, it saw it as a swipe and wanted to delete the book. I moved to iBooks after that. But now iBooks is displaying irritating tendencies, it's all open again. I'm not going to use an app that will throw away books from my sources and keep the "official" sources. So iBooks is now out. I'll go back and look at BlueFire, but I'll also look at Marvyn. I started looking at that earlier, but now I think it deserves a better look.
I don't require much in an epub reader. Folders, non-twitchy UI, and not throwing away my books when it feels like it. That shouldn't be hard.