The judge is a real weirdo. Remember the hearing where he called Flynn a traitor (I guess for working as a lobbyist for Turkey, how that is treasonous I never understood).. and then took a break, and came out and said "hey, sorry, about that treason thing I said - scratch that".
At times he's seemed very pro-Flynn, and at times very anti-Flynn. Regardless I don't think he has any choice.
It's like a cornerman throwing in the towel in boxing. The fight is over, but it's not officially over until the referee acknowledges that the towel has been thrown.
Judge is unpredictable.