Either one side or the other is lying about this. Typically, the government would get a proffer from the witness laying out what he was prepared to say.
Typically indeed but the sequence of events does not always allow it. Ideally, you figure out what you have for cases and line up your witnesses and extract various agreements to give some benefit/incentive to a cooperating witness.
The problem here though, is that Flynn's case has been ready to go for ages but the government has held off on seeking sentencing because they wanted Flynn to cooperate on his partners prosecution and they were still developing the case to see what they had. Flynn was able to agree in advance that he would cooperate fully along the way- and contends that he did- but was not able to foresee in advance what they were going to require him to testify to in the end. So he argues that he met his obligation to cooperate but that obligation does not require him to testify to anything untruthful which the prosecutors developed after he agreed -in a general way- to cooperate.
The Flynn case has been scheduled and rescheduled and rescheduled and rescheduled for sentencing so many times you would need an app to follow it. And the government keeps coming up with a new need for him to help prove what they are not able to prove against his partner. It's ridiculous.
My view, as always, is that the judge should let him out of his plea agreement and just let him go to trial. Mueller's team pressured him into pleading by wearing him down financially and by telling him that the ones who investigated him (Strzok was one) concluded that he lied. Later it was determined that investigators said in their reports that they did not think he lied. That is flat-out another example of Mueller and Weisman not turning over exculpatory evidence.
In addition if they went to trial, by the time they get there the fisa/dossier background info will be available and Flynn can use it to show that he was wiretapped and investigation was launched into him upon a deficient warrant, and as a result of the government foisting a fraud upon the court. But no, the government is using the bullshit case against him to squeeze him to prop up their bullshit case against his partner. This shiite needs to end.