I rode over to the Cherohala Skyway this morning, and it goes up over a mile from sea level. Most of my riding is done between 300 and 2200 feet.
I had my ear plugs in, and when I descended, my ears started hurting. I also noticed that I was hearing some noises that were different than usual. I flipped up the face shield, held my nose, and popped my ears. I guess I must have gone deaf at some frequencies from the overpressure, because as soon as they popped, the bike sounded totally normal again.
The Cherohala Skyway is nothing compared to the elevations you see in the Rockies. The guys that ride there are probably a lot smarter about this stuff than I am. However any time you have elevation changes of 3/4 mile or thereabouts, you've given your bike and your body something to think about.
FWIW, I've had the ecu recall done, but I thought it felt like it took the bike a while to richen up after the descent.