I would research this a little farther if I was you.
A recent bug in the Arduino PWM libary code was found such that if the PWM duty cycle was set to 0% there would still be a very small positive pulse output, in other words the duty cycle could be changed only from 1% to 100%, but not 1% to 0%. This was fixed in the next upgrade to the libary code but the temporary fix was to just test the duty cycle value and if less the 1 then write a 0 to the outout pin. So in that case a digital output instruction was overiding the normal PWM output.
Not saying that this applies to your processor chip or your software routines that support the PWM module, but the real answer should be in the the data sheet for your processor chip. Or you could write a simple program to see if doing a direct output instruction would overide or effect a ongoing PWM routine.
Lefty.