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...which also by nature need to emit some sort of signal--RF, acoustic, EMF, optical--which should make them easier to detect than merely intelligence gathering sensors.

My suspicion is that the hurried retrofitting of the aircraft means that it does not posses the full defensive capabilities of the VC-25A and someone finally lost enough sleep over it to grow a spine after seeing how effective Iran has been with the very limited resources they still have. Believing a handheld rocket of some sort could bring down the underdefended Graft Force One is likely what caused this panic.

It is also interesting that "passengers on the aircraft were instructed to keep their windows down during the flight, and according to flight data, the plane carrying the president did not turn on its tracker until it was over the Black Sea near Istanbul." ( https://abcnews.com/Politics/secret-service-urged-trump-depart-turkey-air-force/story?id=134606227 )

Why did passengers have to keep their window shades down?