Yeah. Copying new versions on top of old versions is not intended behavior. I cannot guarantee that the game will work properly if people do this, though I can't really imagine why it wouldn't.But why though? It's not really the intended use, because you can end up with dead files hanging around, especially cached bytecode which can create conflicts.
Evangelion-01, are you sure you didn't just extract everything into a subfolder of your original install, leaving all the original files untouched?