In the last 2 weeks my TMCC NYC Mikado and my Flyer Chief Erie Berkshire both were operating fine and then suddenly began misbehaving.
The Mikado had been operating for about a half hour and then, suddenly would not back up. After letting it "rest" for a half an hour, it would not go forward as well. The troubleshooting guide in the manual said I should reprogram the engine.
The Berkshire was performing flawlessly and then suddenly, did not respond to the controller, although it functioned perfectly under conventional control. The troubleshooting guide in the manual said I should remove the boiler and look for loose connections.
I looked at how to accomplish each of those operations, then I decided to look at the batteries in the remotes. My multimeter indicated that both sets of batteries had 2 cells that were "borderline", and the remainder were okay but not 100%. None of the batteries were in the "replace" range according to the multimeter. After replacing all the batteries with fresh ones, both engines worked perfectly in command mode.
So my take home lesson, despite what the troubleshooting guides have to say, is to replace the batteries in the controllers BEFORE you disassemble or reprogram anything.