I think it would need to be a mechanism similar to how user moves are handled where the old thing sticks around forever but has a field that says "the new one is over here" and then the new one has a field that says "yes, I am the same as that old one". At least I think that's how e.g. mastodon handles moves of users (just the person/actor, not any of their content. AFAIK nothing in the fediverse can do something like this with anything other than a person/actor at the moment)

OR, after changing the ID, have the instance publish a "domain_change_notification" that all federated instances would be listening for and then they would update their data.