I am new to the CVO world, but have been hanging around HD V-Twins for a long time. I know for a fact that doing what you did increases airflow, therefore leans out your engine further. I presume that with our newer engines already running lean and hot for emissions, things can get really toasty. I have seen many instances of motors running hot, sometimes getting damaged. The only way you'll know for certain is to get an oil temperature gauge and compare numbers before and after.
From my experience, the results have always been the same. Either rejet or reprogram. For my money, because the results are always the same, I would go ahead and reprogram.
I recently did the Fulsac 2.25 cores, Sport Pipe, and TTS ECM download. Only completed the job Friday and only a few hundred miles so far - but the results are remarkable. Less heat, greater power and throttle response, and sounds really nice. Not sure about MPG yet, but I anticipate the same.