I’m no lawyer, so I don’t know how this works, but I think part of the point is that Flynn was unfairly coerced into pleading guilty. This is the bed that the prosecution made. Let them justify the current situation. If Flynn withdraws the plea, then the game starts all over and it becomes a whole new thing. I don’t think that helps Flynn as much as the current strategy which seems aimed at highlighting prosecutorial malfeasance.
You have a good point and his lawyer is making a good effort. But the judge asked him in the past did he want to withdraw his guilty plea and the answer was no. He’s still facing the problem that while asking the court to throw out the charges he hasn’t withdrawn his guilt plea. He’s claiming his innocence but he is before the court as a person who has pled guilty already. He may need to risk withdrawing that plea.