Interesting question. I think that it would not work with the processing area, because they will be combined to exclude whatever surface they were excluding before, e.g. you exclude the surroundings in one project, it will also be excluded in the merged project.
What comes to mind, is to always make sure that the GSD of one flight is not more than twice the GSD of the other flight. Otherwise, the software has some issues matching the keypoints from both flights. More about that in this article: Can Pix4Dmapper process Images taken at different Flight Heights
Something you could try is to remove the images that cover the old village in the high flight, but keep some overlap at the beginning of the surroundings between the two projects. You can process the two separately and then you can use the overlapping area to merge these two subprojects without having the high flight mess with the details of the center of the village.
What do you think about that?