Since you already have a reply from the legal side I'm not going to say much other than a consultation is not a bad idea. This question has many permutations and is hard to answer in a straightforward manner. You state they have a special issuance, not a SODA? I ask because a SODA would not follow the airman up to the next class but a special issuance would, as it is associated with the airman's PI number. Is the airman in danger of failing because of a new condition or because of a condition already addressed and if a new condition is it something that say would disqualify for first class but not 3rd class? All of this aside I would opine that generally if you apply for a higher class and for some reason are deferred you are allowed to fly under your other privileges as long as you are complying with the FAA requests for information. If you stop complying and you receive a letter asking for a return of your medical (a denial essentially) then that would apply to all classes.
Aaron Florkowski, MD
FAA designated Senior AME
www.kansascityame.com