I have been doing some reading and research into whether it harms the owl to use your flash. With all of the opinions circling around the forum i tried to find some clear cut answers scientifically but really they all were just opinions. This was the best link i found.
http://photo.net/learn/nature/owlflashIt seems that what is a definite no no is taking pictures of owls at night especially if they are flying. When using a flash you can temporarily blind them hence causing them to hurt or kill themselves by flying into something. It only makes sense. If we are sleeping in a dark room and someone turns the lights on you are temporarily blinded and your eyes take a while to adjust. In the link it quotes a Professor on vision who states that birds retinas can handle very bright light like the sun which is far brighter than any camera flash. So its not likely that during the day a flash would harm an owls eyes. The problem is more that you could startle the bird into taking flight while being temporarily blinded if the flash was taken straight on, thus causing the owl to hurt itself.
I really posted this because i was feeling bad one gloomy day after taking a couple of pictures of an owl i decided to use my flash because i could not get a good enough shutter speed. I took two pictures and to be quite honest the owl didn't even blink and seemed unfazed or startled (i will probably pay for saying this). Although the owl was unfazed i wasn't because i felt bad afterwards that i did it just to get the better pic which it was.
As for getting too close or causing an owl to feel uncomfortable who really know that. Only the owl. Obviously trying to walk up to it and pet it is too close and like others have mentioned with a 400 or 500mm lens how close do you really need to get unless you want to look inside its head. I have been off on a hike and seen a owl or hawk fly off before i even saw it and it was 100 yards away. I have been walking through the woods with my head down looked up and there was a barred owl sitting on a branch 10ft in front of me 6feet off the ground and he did not seem to care as i slowly backed up a bit took out my camera and took some pictures.
I have a huge love for nature and i love to be outside so i think the big thing is to show the animals respect and look out for their best interests.
I probably will not use flash again but i still am in doubt as to whether it harms them during the day
Cheers