Sorry, I'm not sure if you're talking about airbrushing over a cookie that had first been stenciled using airbrush color, or one that had first been stenciled with royal icing (you can do either), but I think Laegwen probably interpreted this the right way . . . correct me if I am wrong! Laegwen, yes, you can definitely stencil with royal icing and then airbrush the raised, stenciled icing. It doesn't seem like people often do this for whatever reason, but if you wanted to apply a quick luster sheen, for instance, to a raised royal icing stencil, this approach is faster/neater than painting on luster. I use a relatively thick icing for stenciling, so I can spray it almost immediately without the sprayed colored settling into the icing (and possibly changing it) too much; the icing certainly doesn't get disrupted by the airbrush spray because it's so thick. But I would still wait and let the stenciled icing dry more completely. As Laegwen said, it's just more efficient not to be swapping tools on each cookie. So I'd stencil all with royal icing first, then come back and re-lay the stencil on top and then spray them all. Anyway, I hope I've answered the original question. There are probably other takes on this too! 
Thanks for the detailed description, Julia. Though airbrushing is still in the hazy future for me, it is good to know that it is possible. But I doubt my hand is steady enough for this - I find it very hard already to hold the stencil in place without accidentially moving it and ruining the design. If I only think about changing tools in between, my hands are starting to shake right away... 