I thought about putting this in the feature request section but it is such a fundamental thing that I have decided to call it a bug.
Whenever you adjust the shape of the polyline while planning, the flight direction setting is destroyed. The "workaround" is easy enough, either never set the direction until you are absolutely sure you won't make any adjustments to the polyline. Or, make a note of the directions and reset it to what you wanted after adjusting the polyline.
A better approach would be for the devs to give us a lock toggle that will hold the direction setting while messing with other adjustments. This must take extra effort to code because the Map Pilot devs have the same problem. Let's see who can address it first !