Yeah, I'm not actually sure on the physics and chemistry of it all, but when butter clarifies (separates out into liquid and cream), it doesn't recombine well, and behaves different when it is baked. A lot of baking recipes (like cookies) depend on the fat melting as it cooks to give the food the right texture. So the taste probably won't change, but the shape and consistency probably will. I guess it depends how picky you are.