>>Boofta, oh no, you let the cat out of the bag !, perhaps you shouldn't have said the "actual controls are in the flightdeck" - oh no, thoses security boffins will have to think of something to deny us access to the flightdeck !
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Might the answer not be to have the automatic control system protected by a password system, so that even if wannabes gained access to the flight deck they'd need to know the security code before they could over-ride the autopilot and take manual control? Likewise, under manual control the pilot could be required to input a sequence of codes to the keypad at random intervals otherwise the system would revert to automatic control.
That would stop any hi-jacker taking over control!
To obviate threats to the crew to divert from the planned route the code sequence could include a hidden lock code which would render further manual input impossible.
There! Problem solved . . .
System could be unlocked by a transmission from ATC (again against a pass-word sequence).