I was just about to restore my non-iBooks ebooks from my backup disk, but apparently I had excluded the Music folder from Time Machine..
They were still on my iPad, so I tried to sync them, but it deleted them from the iPad instead. Ugh.
edit: They're in the MobileSync folder in the Library of the backup disk. I grepped for a few unique terms and got results. But they're in some kind of obscure format. No idea how to get them out of there, yet.
I've got them back. I was not able to extract them from the iPhone backup, but I found them in ~/Library/Containers/com.apple.BKAgentService/Data/Documents/iBooks on my Time Machine backup. The epub files do have random names now, but fortunately most of my files were PDFs anyway, which have their original names. Phew.