“So I think the question becomes: Can Congress take away the President’s Commander-in-Chief status?”
– That seems like (yet another) different question, to me. Conviction in a Senate trial after impeached with the intent of “removal from office” (q.v. US Constitution, as discussed above), which certainly includes POTUS’ “Commander-in-Chief” status.
But hopefully you understand that POTUS’ “Commander-in-Chief” status doesn’t prevent the military from reacting to threats. Authority to launch new attacks as part of new missions when not at war and not part of an already-authorized operation, does rest with the POTUS. But non-nuclear defensive actions, and command within the context of existing situations for which there are operations, rests with military command.
You started this tangent with the idea: “Shutting down the President would leave this country absolutely defenseless. I can see Russia, Iran and China salivating at the prospect!” And I think that is not true, unless any of those countries are actually on the brink of wanting to attack the US, which I do not think is the case.
And on top of all of that, change of POTUS has by now been considered very carefully for decades now, and I am sure that:
1) A new CIC would be appointed at the same time a POTUS is removed.
2) US Strategic Command has already decided what it will do in case of many different types of crisis, when the POTUS and VP and Congress are not in communication. For example, if a nuclear bomb takes out Washington D.C. and then we see some nation attacking us, I have no doubt our military would respond decisively, and worry about the legalities later, if there’s anyone left to worry about those.
3) Given that the US military could see Trump was a dangerous chucklehead, at least as soon as he was the Republican candidate in 2016, they would have started thinking about “WTF do we do if this guy becomes POTUS and acts like a loose cannon?”