If you have deleted the hidden code then it might cause some problems as it looks like that could be the code that prompts you to set up your manager details when you first load the game (or after you have deleted your preference files) though I have no idea if the game will just skip past those screens, through up an error or just crash. (Though it might not even be possible to get that screen with a custom skin as it pops up before you have a chance to even change skins, you might want to try