PKHex changes not showing up in pokemon Y

[fishkins]

so i’ve tried to do two changes, first the complete pokedex and add a few pokemon to my box. neither of which show in game, but everytime the file is loaded back into pkhex the changes are still there no matter how many copies i make/click export.

when i made these edits to the ‘main’ file i just replaced the original, so it’s the only one i have, there is no ‘main’ file left without the changes

i’ve tried removing the edited ‘main’ file from the citra folder where the save was, by moving it to a different folder, but even though the citra save folder was empty the game still ran like normal and let me save. i thought maybe the completed dex wasn’t working bc this is a brand new save with only 1 badge, im just trying to get shiny charm, so i tried adding a few pokemon but i couldn’t get that to work either, i have no clue what to do because i honestly have no idea what save this thing is even using at this point if it’s not in the citra folder and i can’t check where you normally would right click “view save location” i think it says in the directory cause i don’t have game folders only the .3ds file so i open the game from files. im not using save states at all, manually opening game everytime, if i need to reset the whole save because i messed something up i can but how can i get the complete dex feature to work?