NopeInserts

Recently I've been playing around with editing Pokémon base stats through tools like DSPRE. However, I've been running into a slight issue; I've been having an issue where when I edit a Pokémon using PKHaX/PKHeX and place it back, it reverts the base stats to the values before the DSPRE edits, is there a way to circumvent this or am I stuck with this? Is there a way to edit the base stats PKHeX works with? Or will I simply have to be patient and grind out EVs and friendship?