I'd like to also report that this still works! I originally booked two PE (G Class by luck lol) Virgin tickets via Delta and I was able to upgrade to UC with just 25,000 SkyMiles per person (LHR to BOS).

Similar to some posts above, I went through one chat agent and three phone agents before finding one that knew what she was doing. Here was my strategy:

After my unsuccessful attempts with the one chat agent and two phone agents (they all either said that they were not able to do anything because its a Virgin operated flight or said that I can only upgrade with cash and it would be $1,000+ per person), I told a little white lie to the third phone agent. I told her that I had just spoken with a previous rep who had told me I could upgrade my PE Virgin flight using 25,000 SkyMiles and (thanks to the advice given above), I also immediately gave her the VS Flight #. She put me on hold while she spoke with another rep but after about an hour (she had to verify my fare class) she had me booked in Upper Class! She also initially mentioned the luxury tax aka air passenger duty but eventually told me that it's actually not applicable because I had paid for it with my original PE booking (as already mentioned in this thread). Good luck!