This is kind of a big deal for any autopilot. If you use ardupilot with a data link and upload waypoints during flight (which is a standard feature for any autopilot) the unit stops flying the airplane and it is just free falling until the upload is done and then autopilot kicks in again and tries to save the plane. In our tests we had 10-20 waypoints and the "blackout" lasted about 5 seconds, which might or might not be enough to crash the airplane. However I don't know if this time is going to increase as you increase the number of waypoints.
Am I the only one who noticed that?