I require a gluten free special meal and have that in my profile. The request for a special meal has no effect on the upgrade process. Without exception, when I have been upgraded less than c24 hours before departure, my economy meal main course has been re-plated for me. But then, the economy meal is better than the Business meal, so I'm not complaining. Incidentally, the FAs are generally clueless when it comes to special meals, so you need to stay in control of every aspect of the meal service.
As I understand it, this process is different on other airlines. I know for a fact that, with BA, a special meal request will stop an upgrade processing after the catering is set for a flight.