During night flying, which color lens for a flashlight is most beneficial?
You will want to use red light.

Why?

See Does red light preserve your night vision? on the Biology StackExchange for a good explanation of the biology and physiology involved, and how it relates to perceptual ability.

As stated in this answer (by leonardo) to that question:


  If one is exposed to red light (above ~650 nm), it would activate the L-type cones mainly (possibly some M-type activation), but no rod activation. Rods are the low light receptor cells in our eyes, and as such, are very sensitive to the photon density, or brightness, entering the eye.
  
  This is just my speculation, but I think it's plausible that if you were in a completely dark environment with just a red light, filtering out the higher frequencies, night vision could be spared in the sense that we don't activate the rod cells.