I have used flash on many setups over the years with no detrimental effect on the birds, they soon become accustomed to the brief flash. At one time nearly all bird photography was done with birds at or near the nest, there was really no option for ordinary mortals, a large telephoto lens (500 or 600) would need a second mortgage to obtain then. The only alternative was to use a flash setup and a lens of about 300mm with extension rings attached to focus in closer, usually as close as 2 metres for a small bird like a Robin. The electronic flash set up I used was an homemade one running at 500 volts, couldn't use that in the rain, it could take up to 3 heads and had quite a hefty output, some of the resulting pictures were superb and many have been published, (pity I can't upload them here, birds at the nest are banned!). When small powerfull electronic flash units became readily available it was easier to transport to some of the out of the way places I used to work, I wired these flashes up to run from a 6 volt motorcycle battery, that enabled us to use the setup for prolonged periods without having to get out of the hide to change the batteries! We had one hide on a Peregrine for over 3 weeks and the battery lasted the whole way through to the young fledging. Flash units are far easier to use now and are capable of automatic light sensing and cut off to allow quite sophisticated setups using several heads at once. No more measuring the distance to each flash head and doing a mathematical equation to determine the correct f stop, now you just set the f stop you want to use and the flash/camera does the rest! If you set the flash correctly it can be difficult to tell it was even used, I now use a flash extender on my SB24 when shooting from the car window, you can use it from a hide as well of course. I've had some great results on seabirds on the seacliffs using this setup, some are at quite a fair distance, but the flash + extender gives out enough light to lift the subject and give it an highlight. You need to persevere with flash, once you have it sussed you will wonder how you managed to photograph birds without it.
nirofo.