Each GPU power lines and powered riser are linked to the same GPU, so if a PSU fails, the entire GPU will shut down (riser + power lines).
What would happen if my secondary PSU (the one with only GPUs linked) fails? I.e. 6 GPUs are only connected to the mobo using the USB3 cable to the riser, but riser power and GPU power is cut.
Will or could it harm my GPUs or mobo? How "independent" is a powered riser, power-wise? Will the GPU attempt to draw power from the mobo?
it won't harm your mobo or GPU, unless the power loss causes some sort of huge spike. I use 2 PSU's on all of my rigs and have never had an issue