Every time I use PKHeX It will corrupt my save file for Alpha Sapphire. I used a checker to make sure the Pokemon was legit/legal (would it still corrupt it if it wasn't?). My back up save file works fine and the game will load no problem. I'm at the part where I'm heading through the forest to the first gym. I try to put the Pokemon in Box 1. I've tried making it like I received the Pokemon from someone else and also tried making it seem like I met the Pokemon through hatching an egg from Diamond and Alpha Sapphire.
I've tried searching for something like this but nothing much came up that helped.
If any screen shots or files are needed just let me know, I'll add them.