I can speak only to the AF policy, however as the companies are harmonizing their procedures it is likely the same.

Aircraft are loaded with the number of meals roughly equal to, or slightly above, the expected number of passengers. This avoids wasted meals and expense. When economy is full, they will cater meals equal to the capacity of the cabin. So, if a person with a special meal is upgraded, their special meal would have to be served to someone in economy who didn't order it. Depending on the airport, it is sometimes easy to readjust catering requests at the last minute. However this is not usually the case.

The AF check-in system will not include any names on the list of potential upgrades which include special meal requests.