Okay I am deleting me first response because I didn't look at your video, I just assumed, and assumed incorrectly that you were talking about rolling shutter problems. The flicker you are seeing is caused by lens flare because you have no lens hood and the sunlight is coming down through the props. There's a great deflicker plug-in that will probably fix your shot.
In case you're wondering about what I said before, I had assumed that your problem was caused by Rolling shutter problems. The best way to solve rolling shutter problems is to shoot a high frame rate then run warp stabilizer or a rolling shutter repair plug-in. There are several to choose from.
Thanks for the reply. Not sure if I agree with the sun coming through the props.
I say this because even in cloudy conditions with this particular UAV, I still have similar problems. And it also comes and goes. Balancing my props will go a long way to helping, but the video is already shot. I was shooting at 60fps @ 1080p resolution, which is the best I am able to do.
Thanks for the plugin suggestion, I will try it out now and see how it works out.
Hi Rick, thanks for the awesome suggestion.
Flicker Free plugin worked beautifly. There is no more flicker and I now I don't have to go back out to shoot it again!