I am unable to remove the PlaceMarkers from old mission in any way possible. Unistalled, tried deleting the Mission Planner from the ProgramData folder, even tried removing the entries from the registry. Using Windows 10 Professional OS.
They are stored in the poi.txt file in Documents/Mission Planner folder.
You can delete the file, or if you just want to delete some of them move the cursor over a point and right click Add POI/Delete