If he is not eliglble to be POTUS, he can can’t be commander in chief. The Joint Chiefs would go to the Congressional leadership (such as it is) and lay it out. He goes or we REALLY start defending the USA.
BINGO!
If Obama’s birth was found not to be in Hawaii things would quickly spiral out of control.
All military officers, starting with the Joint Chiefs, take their oaths to the Constitution. You’d have hundreds if not thousands of Major Cooks challenging deployment and other orders.Chaos would reign.
Chaos would also ensue in the civilian sector as you’d have millions who’d refuse to pay federal taxes to a government or obey laws signed by a usurper.