My changes aren’t syncing to my y save

[Shokimei]

I’m using pkhex to bring Pokémon from my black save to y, but whenever I do the transfer, it doesn’t sync to y, but it saves in pkhex, is there something I’m doing wrong, all I do is move the Pokémon from black to y, then go to the pokecenter to see if there in the box, any help is appreciated 

[theSLAYER]

1 hour ago, Shokimei said:

I’m using pkhex to bring Pokémon from my black save to y, but whenever I do the transfer, it doesn’t sync to y, but it saves in pkhex, is there something I’m doing wrong, all I do is move the Pokémon from black to y, then go to the pokecenter to see if there in the box, any help is appreciated 

If you reopen the save in PKHeX (after editing the save and closing PKHeX), are the changes there?