Yeah, the simplest solution is to just have the savegame import the new version of the Workshop blueprint again with a new ID every time it notices the Workshop blueprint has been updated. This would preserve existing constructions in a save-game without causing weird issues. Simply make the old version not be published in the exchange anymore.
At worst it would mean that if a Workshop blueprint is updated a lot, it might create a lot of old versions of a blueprint in the savegame. So maybe some garbage collecting of old versions of Workshop blueprints when they aren't used anymore.
It would also mean that unsubscribing from a Workshop blueprint wouldn't damage anything in the savegame, but it would unpublish some blueprints on the savegame's exchange. If garbage collector then sees that the unpublished Workshop blueprint isn't used in the savegame, it can delete it.
At worst it would mean that if a Workshop blueprint is updated a lot, it might create a lot of old versions of a blueprint in the savegame. So maybe some garbage collecting of old versions of Workshop blueprints when they aren't used anymore.
It would also mean that unsubscribing from a Workshop blueprint wouldn't damage anything in the savegame, but it would unpublish some blueprints on the savegame's exchange. If garbage collector then sees that the unpublished Workshop blueprint isn't used in the savegame, it can delete it.