When AreaScan is used, UgCS places extra waypoints to keep the flight path at a constant altitude above ground level. However, once the route is converted to waypoints, this functionality is lost. There needs to be a way to either convert the waypoints back to a route so the draping can happen again, or have a command to apply drape to segments. This would command UgCS to add waypoints along the segments to maintain height above ground.
I've also needed this when I import a CSV of endpoints, but there is no way to get the drape unless I manually add waypoints along the route. Please add this to your list of feature requests.