The coarsest overview should cover the entire area as it should match the boundary file. I would consider with your modified boundary, redefining and rebuilding all of the overviews. It appears as if the overview you have indicated is only a partial and has not caught up with the entire dataset. Have you tried deleting the overviews and re defining them?
If you have tested that procedure then I recommend creating a Support incident to determine what may have happened. I have not had trouble creating mosaic datasets at SP2, then rebuilding the footprints as you have done and not lost the coarsest overview.