Mine didn't switch either. Probably because the SD channel was on 9249 and the HD one is on 5155. (Gee thanks Dish! It's Eastern Arc, so why not just re-use the number?)
But here's the part that I really don't understand. After setting timers for the new channel, I went back into the timer list to delete the timers for the old channel. I found the first program right away by looking through the list for SD channels, because there's only one other timer that I had on any other SD channel. When I went to look for the rest the same way, I couldn't find them at first -- there were no other timers without an HD icon. When I went back through it slower looking for the program name, I found that the rest of the timers for the channel in question, even though they weren't set to record any episodes, now sported an HD icon! If the point of using two different channel numbers was to avoid confusing the receivers (and I can't think of any other purpose it would've served), it looks like they failed...