Bruce, the average is over several images and is just used to decide whether to focus because the FWHM has grown enough. I have to stress that PP is no it a photometry tool, so flux and FWHM measurements are not anything like science quality. You’ll need to look at your images with a real photometry tool and see how they look, how the flux measurements are etc.
But here’s something you might like: If you put #defocus nnnn into an ImageSet, it will refocus by nnnn counts for all of the data images in that image set. This is commonly used to spread the light out over “enough” pixels. See Scheduler Help and search for Defocus.