To start, I would have him get a copy of his Criminal History to see what is actually on it.
It sounds like he is not a prohibited person, but does have a felony conviction on his Criminal History. His pardon may not show up on that. Maybe his Criminal History Record can be ammended to show the pardon, but you cannot get the record expunged.
He could also Appeal to a Circuit Court under 175.60 9(14m).