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Screenshot from game Light and Dark Images Light and Dark Masks I haven't gotten it working in the plugin but using GIMP and applying dark mask as a layer mask (darker equals more transparency), I got the resulting image where you can see the blue dot from the machine is showing up which is evident in the game screenshot of what the profile picture should be. But I still haven't figure out how the light mask is used. Joined Image

If you're willing to do modifications with PKHeX or any other third party software, your Pokémon can not be legit. Legal at best. Legit is something obtained legitimately in game, that remains unedited. Anyways, this should be the tutorial you're looking for.

That is correctly illegal, PKHeX is working as intended, it is not "100% LEGAL". Why do you think your starter pokemon should have a move that is only learned via breeding, when it was never an egg/didn't hatch from an egg with parents that knew that move? Move legality is determined by the encounter details, not just "the species can learn it, so it's fine". If a move is learned via breeding, it has to be learned via breeding, not by you editing it onto something that was never an egg. I also can't replicate the Geodude issue at all, the one I caught ingame and the one from the encounter database both appear legal. Either you modified it to make it illegal, or you used glitches that changed some value. Please provide a pk2 file for it as well.

Installing custom firmware: https://3ds.hacks.guide/ Extracting your savefile: https://projectpokemon.org/home/tutorials/save-editing/managing-3ds-saves/

So there were just extra bytes for some reason? Bit weird, but I guess it's better than inexplicably missing data, lol. In any case, I re-dumped the save after doing the same thing I did on emulator (saving the game with no changes) and it came up clean this time, so I guess it must have just been a weird fluke. Thanks!

EDIT: Problem solved! Refer to my guide for details if you've encountered the same problem.