That's certainly a possibility, but I'm hoping we can do better than checking first and then aborting a split if the situation is found. We
should (he said tentatively--not having examined the code in question

) be able to handle this in the Link Update routines. So that the new file name is included in the href whether the target fragment/id is present or not. At least I
hope so, anyway.
It's worth pointing out that Flightcrew doesn't report the "Fragment identifier not defined" error like EpubCheck does. Probably a big part of the reason this issue has escaped being nailed down for so long. And it's been around a looooong time.