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.
 
	 
				 
 
		 
 
		 
 
		 ((( WAHHHH
((( WAHHHH
 
 
		