It’s quite rare for a theory to be dismantled so thoroughly that we look back on it and say “oops, all of that was just coincidence”. Rather, the existing theory is a special case of the one that replaces it.

For instance, Newtonian physics wasn’t demolished by Einstein et al. It was refined, such that Newtonian physics applies very well in scenarios and scales that we would consider ordinary.

But you are completely right. When the theories are unified then people could very well be saying “you can’t just add these states together”, just like I’d often say that when talking about adding speeds together (it doesn’t convince the traffic officer). What I do think, though, is that a perfectly good response to that will be “ah, yes, that isn’t a problem though because this isn’t in the presence of a magnetic, rotating, supermassive black hole with a funny hat on, so the flopookle correction we learned about in physics 201 is negligible”