An update. A had a call from Natalia from customer care yesterday to give me the results of their investigation. They found that my J meal was not loaded as it looked like the upgrade did not have enough time to carry my preference from Y to J. I explained that the upgrade was processed 3 weeks before the flight. She also said that my Y meal was not loaded either. She was then a little confused as to why the Y preference would not have carried through to the J booking.
Natalia was certainly apologetic, and advised that the 'team' are aware of my future bookings this year and would make sure it wouldn't happen again. I explained that that is exactly what I had been told in the past, including earlier this year, and that I did not have much faith in that statement. Natalia was not sure what else to do to make sure catering was loaded. Particularly as it had happened more than once. I suggested she make me CL, but she admitted that was above her pay grade.
Natalia offered me 10k points which I initially declined as "I can't eat points", but she said she was going to deposit them into my account anyway. At least they cover the cost of the J upgrade.
I would like to think that my future flights will run to plan, but ...