Well, I finally got the chance to try to load new chain files into the Hudson this morning. Before I did it, I thought I would try it one more time.
It started up fine with the headlight still off and no smoke (and two chuffs per revolution). I had previously done a feature reset (which failed to bring the headlight back on or the smoke back). The coupler slack sounds did not repeat as they had before (perhaps this was a good sign). I was able to turn the headlight and smoke back on this with with the buttons on the DCS remote-this was also a positive development. I tried to set the chuff to four with no joy. I then set the chuff to one, which worked. Then back to two (also worked), then three (also worked) then four (finally worked).
So now everything is working properly and I am going to run the engine and leave well enough alone!