I'm not sure, but I think the desat fault signal would imply that setting PWM to zero would have no affect. If the igbt has failed on, I think your only course of action would be to open the main contactor in the code. But in that case, you could probably just use the hardware overcurrent notification input to the microcontroller. Note the time, and if the current doesn't drop after "x" units of time, then open main contactor. 1/4 of a second is an eternity for a microcontroller, but a car careening out of control for 1/4 of a second means moving forward like 2 inches. haha.
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