If you’re making a radical change in a framework style theme, I would most definitely fork it into a new & separate version. Particularly if it’s going to have a potentially adverse affect on a lot of existing child themes.
I’m sure I could come up with a creative way to warn your users of a change — but that’d be more easily done if you had some “phone-home” functionality, for messages, in your existing themes codebase to provide warnings / news rather than trying to do it after the update.
Perhaps you could do an intermediate update that won’t harm child themes, that also displays news and information about the new version?