Been testing this for a while and figured that I should probably tell someone: Pkhex while editing the GameCube games garbles the Shadow Pokemon data and causes some really weird things to occur.
Attached are the save file I edited and the backup, untouched (I used some action Replay but other than that it's pretty clean.) After editing, the Tyranitar and the Quagsire in my team reverted to shadow pokemon randomly, however the number of purified shadow Pokemon remained the same.
Befor