This does not seem to happen for me without deleting the harness and running Route Wires again in SW Electrical 3D tab.
I had a wire connection that was the wrong dia so I changed its properties in SWE and then even if I ran the Process function again it did not change the wire dia in the 3D assy doc. Same thing happens if I change the wire colour.
I would expect that changes like this would automatically be updated on Rebuild in the 3D model.
I had to delete the Cable harness of all the connections and run the Route Wires to get the changes.