Interesting, I assumed a Catalyst app was still a macOS app at runtime. I guess we'll have to remove the configuration as you suggested (manager.removeFromPreferences()) and create a new one. That does seem to work.
Is there a way to identify such a configuration when we load it from preferences so we don't have to attempt to track it in some other state? I can't see any existing properties that would indicate it's a "bad" configuration.
(Side note for posterity: the need to restart the machine may have been specific to the Xcode debug build; it doesn't seem necessary when the app gets replaced through TestFlight.)