If you do a partial mission and the aircraft does not make it to the red dot at the end of the programmed flight path it will drop a blue marker (abandonment point) that denotes where it should go back to to start.
You shouldn't be able to rotate the mission since it is locked. If you press the unlock button this will allow you to change the missions orientation and modify the boundary markers. Is it possible you are accidentally unlocking it?
Even if you close Map Pilot and reopen it at this point it should recognize the partial mission and ask you if you want to keep the partial progress or not.
Make sure you are using the most up to date version of Map Pilot as well.