FWIW I was really only focused on the impacts on a confirmed upgrade when an equipment change is effected.

With regards to some other possible issues, like a schedule change or irregular operations, things might be a little different.

In the case of a schedule change it was my experience, in the past two years, that an upgrade was protected as UA changed you from one flight to another. However several FT'ers have reported that UA moved them to a waitlist when they effected a schedule change. In the case of irregular operations (weather, mechanical, late connecting flight) I think that you would pretty much drop to the bottom of the waitlist on the new flight(s), regardless of the fare paid (unless you paid for C or D, of course).