In the Flynn case, the Court of Appeals en banc proceeding will focus on that distinction, asking why the trial court in the person of Judge Sullivan should not be permitted to hold a hearing and complete its judicial process before the Court of Appeals gets involved. The best reason for why an extraordinary writ is required is that Judge Sullivan clearly intends to inquire into why the Department of Justice decided to dismiss the charges against Flynn.
As a matter of settled federal law, charging and dismissal decisions are considered the exclusive domain of the Department of Justice. That ordinarily puts such decisions and the reasons and deliberations behind them beyond judicial inquiry. Indeed, since the government and the defendant both agree on the dismissal, it can be said that there is no longer a case or controversy for the trial judge to adjudicate.
Rockingham, it sounds like you're a lawyer as well.
If what Cboldt says is the case - that the lying case is over and they're fighting about the contempt charge, which is a charge brought by the Judiciary Branch not the Executive Branch - there would be no separation of powers issue. The DC Court of Appeals would thus not be bound by its recent decision in Fokker. I have not read the pleadings, but cboldt seems to be up to speed on this. In any event, the Dims are likely going to achieve their goal of muzzling Flynn until after the election.