I did an install for a MG set to convert from 60hz to 400hz last month and at first, ran the supply and load cables in the same conduit. I wanted to run it in separate conduits but because the MG set was outside, the customer wanted the wire run in one conduit (100 feet rigid, sized properly per code). This company did avionics testing and certs.
Well, it did not work so well. The 60hz side was full of noise, so much so that the VFDs on the HVAC were having issues (random tripping, etc). The 400hz side was equally bad. The testing equipment that they were using simply would not work and the instruments could not be calibrated.
I came back out and installed new conduit just for the 400 hz (labeled it as well) and this solved the problem.
Did a similar install a few years back for another company but had a 60hz to 50hz MG set and had the same problem with the same solution.
Take away message, use separate conduits for different frequencies. May not be required as per code, but IMO its the way to do it.