Abrupt movement when new mission is updated

We are flying a Tarot650 and sending it waypoints/ mission from an on-ground computer. Once we push the mission, we change the drone mode to ‘AUTO’. To push a new mission, we need to change to ‘LOITER’ mode and push new mission and change to ‘AUTO’ mode again.

Problem is, we see jerky movement if the previous mission is still being completed and we change to ‘LOITER’ mode. Any suggestions on how to smoothly transition to a new mission?

More background:
We are switching to LOITER mode before every new mission, because apparently drone would not follow new mission if it is already in AUTO mode.

We are updating missions every ~3 secs, and sometimes the previous mission has not completed. In such a case, we wish to throw the previous mission and start following the newer mission.

Thank you