I have NO idea man, sorry. I believe that it's doable since the opposite is too.
Try deleting the Pokémon from the game in a hex editor. I don't know the offsets to each Pokémon, but I doubt it's hard to find.
Simply change the ones you want removed to FF values. Check if that breaks your game or not. Also, remove them from the maps, as that would probably glitch the game out.
If that works, great. If not, tell me and I can help you work something out. =D