Is moving Waypoints during flight OK?


I have a quadplane with a companion computer on board. To make it possible to make the companion computer control where the plane flies, I am currently letting it write updated mission waypoints to the FC during flight (followed by MISSION_SET_CURRENT). This works fine in SITL. I am also checking that I am a save distance from a waypoint before modifying/pushing it.

So my question is simply, is there any way this could have catastrophic consequences during flight?

Guided mode does not work for my use case, wanna stay in AUTO.