Actually, it is pretty safe to transmit new waypoints also during flight to the vehicle (in your case, your plane). The reason for this is that the wireless transmission protocol which ardupilot uses (mavlink) uses a checksum and counter to verify that the message is transmitted correctly (This is for example documented here, or in this blog) .
Therefore to summarize: Yes you can transmit new waypoints via the flight planner software in the way to describe. You can even add new waypoints or modify existing waypoints in the way you described. This method is safe thanks to the mavlink protocol (*).
Even if your wireless transmission link is not good, and you try to transmit new waypoints, only correctly sent waypoints will be accepted by the flight vehicle. If the messages sent by the groundstation are corrupted by a faulty wireless link, the flight vehicle will request a retransmission, so that the groundstation will try to send the message again. You can see this process working, therefore in flight it might take a little bit longer to transmit new waypoints. But this system is design such that it is possible to transmit new messages such as waypoints, changes to waypoints etc to the vehicle WHILE the vehicle performs an auto mission.
Hope this clarifies.
Best Phil
*Safe is of course a relative measure. We are talking about drone technology here, this is not aircraft level safe with a failure probability of 10^-9 but rather something which someone programmed and then people tested extensively (which is why it is so reliable today). Therefore you should always be very careful how you fly your drone.