I'm probably missing something...
Why not simply turn on the lower MOSFET in question, apply your 1kHz PWM signal to the (correct) upper MOSFET and then modulate it using your 0-50Hz signal. In other words, turn the 1kHz carrier on/off at whatever rate you want.

If that's possible or not at the hardware level, ie "route" the NCO output to the enable bit of the PWM carrier is beyond my knowledge at the moment but at such low frequency (0-50Hz) a software (perhaps interrupt driven) aproach sounds more than reasoanble.