choux pastry, keep mixing while waiting for the roux to cool?
I don't mix my pre-egg mass (not sure that roux is the right word here), but I don't have a stand mixer. Leaving it alone works just fine as long as it is uniformly cooled. If you don't mix (or even if you do) make sure to check the temperature in the middle of the lump of dough, not on the outside. 

As SAJ14SAJ mentioned, mixing it will expose all parts to the cooling air, letting it cool quicker. If this matters for you, there is nothing wrong with mixing. It may change the texture slightly in the direction of slightly chewier end product due to some gluten creation, but the difference won't be very pronounced and may not be noticeable at all, because the flour is well coated in fat. 

So, the conclusion: you don't have to mix, but you can if you want to. No harm done either way, and it can go quicker with mixing.