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Regular save edits, like changing learnable moves, changing possible abilities etc, shouldn't cause game lags. All that is likely the artifact of the mind, or the place you saved in (and then the game is trying to boot up and load that area). For save editing to cause any potential game issue, I imagine you'll have to do some kind of crazy edit, and edited yourself into an area that the game can't load, or edited in stuff that the game struggles to load, while writing a bunch of garbage data into other sectors of the save. Basically it all comes down to putting yourself in a situation where the game struggles to load all the corresponding data.

I think what this game really needs, if it ever gets updated, is a NPC that can change natures and help with EV training. I don't know if IVs would be needed since the Pokemon in this game with Hidden Power seem to have their IVs fixed to have a certain Hidden Power type, like Magnemite with HP Fire or Electrike with HP Ice, but we do need a way to change Natures and EVs, especially for the Shadow Pokemon since your only way to get a good nature is by soft resetting, which can be a really painful process starting in the midgame when there's multiple Shadow Pokemon per trainer. Have the NPC be in Agate Village, that's where I'd put it.