I'd leave them where they are for the time being since you'll just be moving the powdery mildew with them for this season. Let them bloom out and cut them back as you normally would, discarding the foliage in the trash and not in a compost pile. And clean up any fallen phlox leaves around the ground so the PW doesn't winter over.

Don't know where you are but you could transplant the cut back plants in October if you have enough time for them to settle in before cold weather. Or you could wait until spring when you see new growth. Either way they should be fine. PW is pretty common with phlox if your weather's been rainy, hot and humid, if the clumps are too thick restricting air circulation, or if you water from above.