The classical arguments for the existence of God are not arguments from natural science, like most modern theistic arguments try to be, but rather are firmly rooted in the philosophy of nature. Appealing to physics or natural science to refute them thus makes a category error.
Deals with existence in general, regardless of the specific objects that happen to exist. What does it mean to "exist"? Do categories exist? Sets? And so on...
Philosophy of Nature
Deals with change in general, regardless of what types of changing objects happen to exist. What does it mean for something to change? Does change occur?
Physics (and natural sciences)
Deals with the specific changing objects that happen to exist, and examines their specific behavior and natures.
As you can see, metaphysics and philosophy of nature operate independently of what the sciences are doing. Perhaps science had discovered instead that reality consists of little triangles that compose everything. Nonetheless, philosophy of nature, in dealing with change in general, would still carry on independently of that.