@BetterRed - I'm sure your backup regime is excellent. I'm also sure that a lot of users' aren't.
Between that and the way EpubSplit rewrites the epub when it outputs it, I'm just not very comfortable modifying the source epub.
My original plan had been to give the PI the ability to split off several new books at the same time. But that's rather complex both for the UI and the user. Plus, everybody seemed pretty much happy with the one-at-a-time version.
I'll think about both some more. And if other people have an opinion on the subject, now's the time to chime in.