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You can make the Pokémon and add it to your party, but it will retain the stats calculated by PKHeX so at some point you'll need to deposit it into the PC since when the Pokémon is in the PC the game does not store its stats and will calculate the stats when viewed or withdrawn. This is different when the Pokémon is in your party since then the game will keep the calculated stats in memory. So ultimately you just need the game to recalculate the stats of the Pokémon and the easiest way is to put them into the PC.

Pkhax has no way to differentiate between a normal and modified rom so you don't need to worry. Just generate mons in the pc and the game will fix the stats upon withdrawal.

This is a bit off topic, but if you go to your profile there is a section for all of your friendcodes/gamertags. On another note, it's not a good idea to post your email on forums. There are bots that scan for emails to send spam to

I'll give it a try thank you! If anything come of it I'll send an update!