I had a similar problem when I filmed a scene by a lake. There was the noise of a plane when one particular actor was talking. When I cut the shots together (used 2 cameras) the sound of the plane came abruptly in and out at the points where I'd had to cut from one camera to the other. Applying audio transitions helped to some degree in a couple of places in the video, but there was one bit that just didnt' work. So I used Audacity to record just the sound of the plane. I faded it in and out, then placed it on another audio track to make it sound like the plane was flying over while part of the conversation was taking place no matter which actor was speaking.
Not ideal but it covered up the otherwise annoying problem enough for the scene to work well.

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