I have not tested this, but i think this should work:
On the last waypoint of your carrier, open up the "advanced (waypoint actions)", then for TYPE choose "Perform Task", and for ACTION choose "go to waypoint". The "To Waypoint" value lets you choose the waypoint the carrier should go next. It will then go to that waypoint and perform all tasks and routes as it would be the first time for the carrier to reach that waypoint.
Here a YT video, this is for ground units, but it should work for carriers too: