In the old days, before the new fangled EUA's there was no problem with getting partial upgrades, you still got screwed on the total mileage, though.

One thing about "direct" flights, you can get extra mileage if your flight is delayed and "leaves before it arrives" when there's an unscheduled change of aircraft. Last year my wife got credit for MSY-TUS as well as IAH-LAS and LAS-TUS. The TUS and LAS flights were in the air at the same time.

In my opinion the practice of assigning the same flight number to more then one plane is fraud, and should be prohibited.