I never had that problem, maybe you either patched the game wrong or you used a cheat to change your trainer name. Making all your pokemon act like traded pokemon. Maybe someone else can help you better.
Oh, thanks for clearing that up. I thought he was trying to troll. But I was talking about if it is possible to expand the amount of boxes in the rom itself. I was curious due to later down the line when there is more Pokemon from later Gens we would run out of space, for those who want to make a living dex, I.E. me.
Is it possible to Increase the amount of Boxes that is in the pc? Because if there are going to have all 4th and 5th gen pokemon in it, I would need more space since I want to store every pokemon in the pc.