I am just now on the phone with an Elite agent who says that whenever there is a change in itinerary, the upgrades can drop and you have to start over again.

Thankfully, she realizes she doesnt want me to go through that headache. So, she is working to keep the upgrades that already cleared!^

Moral of the story, if you are changing anything on a mileage-upgrade ticket, first discuss about "not dropping what you already got".