Well now you are just making shit up as you go. First you said it was in 2 separate courts.
There was only ever one court- the US Federal District Court for D.C. Now you are claiming he entered more than one plea. If you think he did that, then post the second one.
He pled guilty in his first appearance, he doesn't have to do it again just because the judge changes- it's still the same case, with the same court record.
Sullivan's discovery order was appropriate because he was holding the case open. Judges don't formally accept the plea agreement until they sentence the defendant. That's when the defendant finds out if the court will go along with the deal.
A defendant can withdraw a guilty plea right up to the point where the sentence is passed. The judge will ask them one final time if they want to change their mind, he will caution the defendant that he is not bound by the agreement, the case cannot be appealed, and violation of the terms of the plea deal are grounds for an administrative conviction on the original charge.
Almost always, the court will go along with the plea agreement. But they are not required to.
What NEVER happened was Flynn pleading guilty more than once, or to more than one count of the 1001 violation. The only way that would happen is if additional charges were added later, or if the case was dropped and a new indictment was brought with different charges.
There is also the very questionable legal principle of charging perjury in an investigation where there was no underlying crime. Perjury has elements like every other crime, and one of the elements is that the false statement is intended to affect the outcome of a case. When there is no crime, there is no outcome to manipulate with a false statement. They were questioning Flynn about a phone call that was not improper in any way, and then charged him with lying about it.
The FBI's own documents show that it was a pretextual investigation, intentionally disguised as a defensive briefing. They admit that. Charging someone for obstructing an investigation that shouldn't even be happening is not a legitimate application of the statute, which is why they DISMISSED the charges. With prejudice, I might add...