Well, I now feel properly stupid...
I had been attempting to change the chuff rate, perform the resets, etc. on my inner loop (operating from Fixed 2 on the TIU).
The morning I decided to update the chain files (the day that the locomotive started to operate normally), I had moved it to the outer loop (operating from Fixed 1 on the TIU). I was able to upgrade the chuff rate from two to four (first down-graind to one, then back to two, then to three as outlined in a previous post), got the headlight back on, etc. I then decided to put off downloading the chain files to see how it would go. I have run it for over two hours now, on the outer loop with no problems-it behaves perfectly normally). DCS signal strength was a 10 all the way around. I was able to run it from both the DCS Wifi Ap and the DCS Handheld. I put it back on the inner loop and could not find it in the Wifi Ap. I tried the Handheld and could find it, but it operated with difficulty. I tried a Track Signal test, and all I got was a failed test ("Check Track" or non-responsive). I set a different PS3 locomotive on the inner loop with the same results.
It has been a few months since I ran a PS2 or PS3 engine on the inner loop (I have been running a lot of post war/conventional locomotives). In the interim, it appears that the DCS signal has degraded on that loop (it had been almost solid 10's, with an occasional 9).
I will next try swapping the TIU outputs to see if the problem follows the TIU channel or the track and proceed from there.
I feel quite foolish as I was blaming the engine when it was the DCS signal to the inner loop that was at fault. I have been operating DCS almost since its inception, so I d@mn well should have known better.
Of note is that the DCS handheld seemed to be able to find the locomotive in the presence of a very weak DCS signal, when the Wifi Ap could not. Some people on the other thread were complaining that the Wifi Ap could not find issues on one loop, where the DCS Handheld would. It would be interesting to see if there is some slight difference in the Wifi Aps ability to find a engine on a loop with very weak signal, or if it is just a coincidence.
Update: I just rolled the TIU channels for the inner loop from Fixed 2 to Variable 2 and now have the track signal back up where it originally was. I am able to find and operate the Yellowbelly from the Wifi Ap with no issues. Evidently I have a bad signal generator on Fixed 2. I am not to upset with the failure as the TIU was purchased between 13 and 14 years ago and has given good service.
As a side effect of doing this, by moving the inner loop to Variable 2, I have now been able to run conventional trains from the Wifi Ap (which I had not tried before). It works extremely well!