Keeping chapters that are no longer in the TOC list according to the site would break the paradigm too much. I know I've researched it before.
I could help a little bit by adding a feature to ignore books in the library marked with a certain tag so you don't have to remove the identifier:url. I assume users would still change the title, but they wouldn't
have to.
I hesitate because a) I haven't looked through all the ramifications; and b) it's inevitable that someone will set that tag and then complain when when does it's job.
It would be nice, however, to have a one-step(ish) solution instead of: change title
and remove identifier:url
and remove story URL from epub (depending on settings and use).