So.. after re-routing Abernathy Farms to Sanctuary with the provisioner that used to run between Abernathy Farms & Red Rocket instead, I noticed that now both Sanctuary AND RR are connected to Abernathy.

I checked settlements, checked routes (which are very small in the world) etc if perhaps there was a second provisioner.. but to no avail I can't find a hidden provisioner, yet according to my pip-boy screen the trade route still exists.

Edit: So what it means is according to the pip-boy I still have the old route AND the new one aswell.

I have hit this a few times myself. What fixed it for me was to assign the provisioner to some other task, check that both routes are gone in the PB, then reassign the route.