ROM Hack Help Using .cia Save Data in PKHeX?

AbenavxLucario

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Alright guys, so I was able to figure out how to export my save data into a main file and got it loading in PKHeX and all, but then when I click export Save Data it just exports the same one I started with, with no modifications whatsoever, even when I replace the main file or save it somewhere else entirely, it just saves the main file I started out with, it doesn't even change the modified names of the Pokemon. Even if I save over the default main file, it makes no changes to it when I reopen it or when I try and inject the save back into the game. I do believe it is an issue with (my using of) PKHeX, so please tell me what I should do to actually be able to modify the main file. I have included a screenshot of what my Charmander and box currently looks like and what is remaining static, apparently.
 

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