Isn't Game Freak owned partly by Nintendo? 32% I think.The save of Pokemon aren't hadled by Switch Cloud Save (atleast for now) correct, but I think that Game Freak have their own anticheats system, Game Freak it's a big company that always work with N hand by hand, so it's possible that they can send the data to N and ban your Switch.
Honestly, I don't recomend edit the Pokemon save on a legit and connected to Internet unit.