Not 100% true. Since your going online with it I'm sure there are checks in place so you don't have an unfair advantage. In this case I would think there are two checks. One for the game to load it correctly and one for online use. Though people have been using modified pokemon for a long time now. Maybe this is a way for Nintendo to get back at them.
For example comparing your game data with the game data you had during the previous online session?