You just disable it (properties->watch/auto, in the common settings area - 'Get Hdrs' - to 'Off') and press 'Apply' then you enable it ('On') and press 'Apply' again, it will be activated immediately, it will be the starting point.
Sometimes when I am in the middle of sorting headers the rescan for headers which I have set to 60 min starts and totally annoys me. If it would be possible to show a countdown in the status bar I would be really happy.