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The line between a new engine and just a big overhaul of an existing one can be kinda blurry; I remember one of the devs on the Call of Duty series stating once that buried deep in even the codebase is still code for damaging ground left over from the Quake days, even though the engine has been changed so much since then it's considered a different one.

I believe Retro is still using their RUDE engine dating back to Metroid Prime 1, just massively updated.

Making a new engine entirely from scratch is such a huge amount of work that most companies don't bother any more and just update the one they have.