IIRC, the hardware reset initiated by the keyboard only kicks in once the keys have been held for several seconds. Prior to that, the reset is handled by software. That's why if the Amiga hangs and you do Ctrl-A-A, you have to hold it down for several seconds because the software is no longer responding, so you have to hold the keys until the hardware reset kicks in.
I don't know what part of the software controls the software reset, but I'm assuming whatever it is could be patched to ignore the key combination. If I'm right, that would mean that a brief press of Ctrl-A-A would no longer have any effect, but holding the keys to initiate the hardware reset would.
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moto