I don't SDFC often, but when I have done SDFC after being upgraded, the flights that post to my account credit differently. Prior to the Loyalty Program I noted that when I would SDFC after being upgraded the flight would credit as though it was booked as FC. Now, with the loyalty program, the one time I SDFC after being upgraded I was credited based on distance instead of fare. These are just the most recent occurrences that I remember. This seems to go along with the comment above of - AA does not seem to distinguish between paid and upgraded on SDFC.