Hi new_to_due,
I had a go at trying to get dead-time insertion together with synchronous PWM outputs and single pulse output, but it appears that doing so causes the Due to act strangely. I think that combining all three features is straying outside the bounds of what I'd call PWM controller's normal operation.
It appears that dead-time insertion only works if the PWM clock is not divided down, which isn't helpful if you require low frequency output. Also, the output PWM waveforms only work if the channel 0 duty-cycle update register is loaded with zero.
If your intention is to use dead-time insertion for a H-bridge, it might be better to use two asynchronous channels' high (PWMHx) and low side (PWMLx) complementary PWM outputs and adjust their high (DTH) and low (DTL) dead-time insertion accordingly. I'm not familiar with the H-bridge, but I imagine this is how the Due's PWM channels with dead-time insertion are intended to be used.