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I can use Pkhex now, thanks! The solution was just to copy a Main file to pc not the whole folder. Luckily, I don't have problem restoring the save file. Thanks again for your replies.

Mystery Dungeon is different enough from the main series that PKHeX isn't going to support it. Depending on the results of reverse engineering the game, I might be able to write a save editor, but at a glance, the save looks like the same structure as PSMD, which I opted not to make a save editor for because the structure is fluid enough to require a full understanding of it, and not just a partial one.

Gen1-3 events were created by an external process (event machine/device) then injected to the recipient's savegame. Gen4 events onwards send the game the template, which whe game uses to generate the gift when redeemed in-game. https://github.com/projectpokemon/EventsGallery/tree/master/Released PKHeX compares the pkm against the event templates. No templates for gen1-3? Can't compare against what is not available!

I agree with the slayer. I mentioned about saves syncing between emummc and sysnand in my guide at https://switch.hacked.us only way to get your saves updated in sysnand is disable emummc in hekate or use atmosphere over sysnand option in hekate. then just use edizon or checkpoint to inject your updated saves.

typically, saves injected into emuMMC won't magically "sync" with your saves on sysMMC. Even if they share the same profile, they're treated by the switch as separate profiles. Only way is to boot CFW into your sysMMC, and that typically means not having a emuMMC.

I can help you , my FC is 1908-3660-4711 . But you should know , mystery gift pokemon can not be nicknamed by player , and are you sure that you want a serious Beldum instead of Jolly with 6V AS252 ?

yeah it doesn't look like a PKHeX issue, but instead a bad card or bad card reader issue. It seems that your SD card/SD reader keeps popping in and out of existence for your computer. The only advise I can think of is.. make sure the file exists long enough for you to copy. If it continues to be erratic, consider a new card and/or card reader.