In order to change the behavior of a unit currently following some waypoints, it is not enough to use deleteWaypoint.
To achieve the wanted effect, you should rather use setWPPos to the unit's current position (thereby stopping the unit), and (after a small delay) use deleteWaypoint to remove the next waypoints.
VictorFarbau
Another (more foolproof) method to avoid the problem of non-deleteable waypoints is to introduce another group (createGroup) and join all units of the present group. A new group will start without any preset waypoints so you can start setting new WPs all over again.
Old group is "_combatGroup", new group is "_combatGroup2"