The way I figure it, you have the light shade highlighting cheekbones, nose bridge, et cetera, and your darker shade recessing cheek hollows, temples, or whatever you've chosen to use it for, and leaving it alone like that would leave your actual apple-y bits of cheek totally bare, which on my face, looks a little flat. It's a matter of taste, but I think blush adds even more...dimension, I suppose, to your face, especially with contouring. I also agree with the above posters, that the blush should be applied before highlighting, and probably shouldn't be the focal point of the look, as that may draw attention to your contouring as well! But if you've blended completely imperceptibly, I don't even see a dramatic blush as an impossibility.
So, to make a long post short, blush seems to definitely be alright to use while contouring!
