The Del-key, if I recall correctly, deletes Stops from the Route Planner from the top down. So if you press the Del-key once, it will delete the topmost Stop in the Route Planner. Pressing it twice would delete two stops from the top of Route Planner, etc.
The feature is not aware if you have already passed the Stop(s). It simply deletes them one-by-one from the Route Planner as you hit the Del-key.