I ended up getting the older pokemon games to show up in pksm you can add items pokemon change stats its pretty sick and I didn't expect it to work with games like crystal or emerald but it just worked lol also I found my save in twilight menu sub folders.
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You could always download pkhex on pc and transfer the 3ds game save to pkhex there are a ton of options you could use to backup your games and pkmn so you can transfer the save or just the pokemon to any of the other games. There are a ton of vids showing how to use it to the fullest
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