Nothing going on here except Flynn wants to disgrace himself further. Even if the full appeals court remands it back to Flynn rather than enforcing the order to dismiss, it just means that Sullivan gets to hear it some more, make a ruling and then the government and flynn can appeal it again through the regular appeal process. Don't be surprised if the appeals court remands it, that Sullivan rules to dismiss and then- as a face saver- says that he was just enforcing his right to finish hearing the case.
Do what he will. Take the short way or the long way around. The outcome will be the same. The case will be dismissed and there will be no need for a pardon.