Care must be taken when taking flash photographs of owls and when shining a flashlight on owls.  A laudable goal is to minimize the disturbance and impact on the owl. It is important to realize that both the camera flash AND the flashlight used to find the owl temporarily impact an owl's night vision.

  • Night vision relies upon the rods in the eye to see variations in the intensity of light.  The spectral response of rods is low for red light.
     
  • Red light has been proven to preserve night vision.  Night-time photographers, astronomers, law enforcement, theater ushers, and others who rely upon their night vision use red flashlights to see in the dark and yet preserve the response of the rods in their eyes.  See http://biology.stackexchange.com/questions/2075/does-red-light-preserve-your-night-vision
     
  • On moonless nights an owl is relying almost entirely on the rods in its eye to see.  On nights with a bright moon both the rods and the cones are used to see. Note that owls hunt mainly by sound (except for the Northern Pygmy Owl and Snowy Owl).

I have researched different ways to photograph owls at night and also minimize the impact of bright lights .   These precautionary measures allow photos to be taken without injuring the owl and minimizing risk to the owl while taking a photograph.

  • Do not use a regular (white light) flashlight.  Instead use a red-led flashlight.  I use a Maxxima MF-37R red-led flashlight to:
    • help locate the owl
       
    • to illuminate the owl while my camera achieves auto focus. (note the auto focus beams on cameras are in the red-infrared long wavelength region and can be used to achieve focus without an additional light source, however often they are very slow to achieve focus).
  • Minimize the time you shine the red flashlight on the owl, move it away or turn it off as soon as you achieve auto focus.
     
  • Use a red gel filter on your camera flash.  This does leave the image with a very red tint and much darker than with no flash filter.  Photoshop and Aperture can correct the color balance in post-processing.  Test this out before going out in the field (put a teddy bear up in a tree).  The filter system I use on my Canon Speedlite flash is a Exolmagin Roguegels-U kit.
     
  • You probably do not need to use a Better-beamer or other Fresnel lens flash extender for owl photography.  Remember these Fresnel lens really focus the light into a tight beam -- something we do not do to the owl!
     
  • Use a flash bounce to illuminate the owl if possible.  Intentionally direct the flash slightly away from the owl, on  tree branches near the owl.  The photos where the flash illuminates only one side of the owl look much better than direct illumination.
     
  • Use a new DSLR with very low noise at high ISO so there is less dependence on a bright flash ( the Canon 5D3 or Canon 1DX set on ISO > 2000 works amazingly well).  Some of my nighttime owl photos were taken with no flash, only a dim flashlight and very high ISO.  The new camera sensors are amazing in this regard.
  • Shoot in raw mode so the exposure can be increased when post processing.
     
  • Take only a few photographs of the owl and allow some time (30 secs) between successive photo flashes.
     
  • Never take an night-time flash photograph of an owl in flight.
     
  • Try to photograph on moonlit nights, when the owl is not relying 100% on rods for vision (the cones are also being utilized on these moonlit nights)

These measures make a big difference.  I have observed owls demonstrating little to no impact on their night vision after taking their photograph at night.  In many cases the owl flies perfectly from one branch to another demonstrating that they are not blinded.

"Flash-lighting" of owls, for photography purposes or for birding, is more harmful in my opinion than the camera flash.  The duration of the camera flash is on the order of 1 /1000 second.  Although the power (watts) of a camera flash can be very high, the short duration from the camera flash reduces the total number of photons on target.  Try an experiment on yourself to see this effect at night.  Have your friend take a flash photograph of you.  Note how long your night vision is temporarily impaired.  Now, have your friend shine a bright flashlight on you and note how long your night vision is impaired.  Impairment of night-vision is often more pronounced by the flashlight than the quick flash from the camera.  Try the same using a red-light.

More discussion on this subject can be found here:

http://www.owlpages.info/forum/viewtopic.php?t=1582&sid=32627e78474959977aea9b98a32cc6ff

http://biology.stackexchange.com/questions/2075/does-red-light-preserve-your-night-vision

http://photo.net/learn/nature/owlflash

http://www.birds.cornell.edu/AllAboutBirds/bp/guidelines