About the Metaverse and the Collective Unconscious

So Mementos and the Metaverse were erased at the end right? But they're the metaphysical manifestations of the Collective Unconscious, so how is getting rid of them even possible? I mean unless the Phantom Thieves destroyed the Collective Unconscious (which would be bad) shouldn't they just come back in some form? Even if it's not in the same form as it was it can't just not exist anymore without having massive ramifications for all species on earth, especially in the universe where it demonstrably exists

Am I missing something or over thinking things? Or does it just not make sense