A single waypoint can be deleted by selecting it and then clicking on Delete Selected from the context menu displayed when clicking with the Right mouse button.

The deleted waypoint determines the method used to calculate the distance from the previous waypoint in the route. Thus, if a waypoint which currently terminates a Great Circle is deleted, the calculation of the distance between the preceding and subsequent waypoints will be determined by the properties of the subsequent waypoint.

In this example, the route and distance between waypoints A and B is based on a Great Circle calculation. This is indicated by the blue curved line and controlled by the properties of waypoint B.

The route and distance between waypoints B and C is based on Rhumb Line calculation indicated by the straight black line and determined by the properties of waypoint C.

If Waypoint B is deleted, the resulting route and distance between waypoints A and C will be based on a Rhumb Line calculation determined by the properties of waypoint C. Those properties can of course easily be altered.  Click on Waypoint C to select it, then Right Click and from the context menu select Toggle Great Circle.

A group of waypoints can be selected from within the Editors waypoint list and deleted by clicking on the Delete selected waypoint(s) option available on the Context Menu for the list.