What if the thermodynamic miracle has no effect on the utility function because it occurs elsewhere? Taking the same example, the AI simulates sending the signal down the ON wire... and it passes through, but the 0s that came after the signal is miraculously turned into 0s.

This way the AI does indeed care about what happens in this universe. Assuming that AI wants to turn on the second AI, the AI could have sent another signal down the ON wire, and then end up simulating failure due to any kind of thermodynamic miracle, or it could have sent the ON signal, and ALSO simulate success, but only when the thermodynamic miracle appears after the last bit is transmitted (or before the first bit is transmitted), so it no longer behaves as if it believes sending a signal down the wire accomplishes anything at all, but instead that sending a signal down the wire has a higher utility.

This probably means that I don't understand what you mean... How does this problem not arise in the model you have in your head?