I'll answer my own question... There's doesn't seem to be a way to automatically update the length used in the cut list. However, I was able to get the newly calculated cut length to show only after I made a manual change to the wire routing. These are the steps I followed after changing the slack percentage from zero to my new value of 5%:
1.) While editing the default (not flattened) configuration of the harness I selected "edit route", and then "edit wires".
2.) I picked one of the wire routes in the "Wire From-To List" and then clicked on "Select Path".
3.) I deleted the current selections, and then manually reselected them in the correct order.
4.) When I clicked on the green check to confirm the path, all of the other calculated path lengths updated using the new slack percentage.
I think going forward it would be better to have the slack percentage associated with individual routing assemblies, rather than as a system option. Otherwise, unintentional path (and cut) length changes could happen if two different operators are working on the same harness assembly and their "slack percentage" settings do not match.