If you have enough empty sky elsewhere to cover the affected part you could use the cookie cutter. Place your video on two tracks, one above the other, in sync. Use Track Motion to move the lower track so that an empty part of the sky lines up with the flare on the upper track. Use the cookie cutter to punch a hole in the upper track where the flare is and expose the lower track.

You may have to do some adjustment to the lower track's brightness and color to make it match. Sky isn't really a very constant background. The brightness changes with angle, so when you shift the image the color won't be the same.