As part of his guilty plea, Mr. Flynn said he knew lying to the F.B.I. was a crime, but he has since said he was innocent. Mr. Flynn is now asking Judge Sullivan to allow him to withdraw from the guilty plea, saying he was forced into the decision. The judge, who carefully walked Mr. Flynn through the plea in 2018, has not ruled on the request.

The newly disclosed notes appear to be written by Bill Priestap, the former head of the F.B.I.’s counterintelligence division, whose initials are on them. Mr. Priestap played a central role in the F.B.I.’s Russia investigation. He approved the opening of the case, known as Crossfire Hurricane, in July 2016 to determine whether any Trump campaign officials, including Mr. Flynn, had conspired with Russia during the presidential election.

The notes were taken on Jan. 24, 2017, only days after Mr. Flynn lied to Vice President Mike Pence and other White House officials about his discussions with Mr. Kislyak. The notes show that F.B.I. officials were debating how to deal with Mr. Flynn and figure out the goals of the interview.

In one instance, Mr. Priestap writes: “What’s our goal? Truth/admission or to get him to lie, so we can prosecute him or get him fired?” In another, Mr. Priestap appears to understand the risks of the interview, adding, “Protect our institution by not playing games” and “If we’re seen playing games, WH will be furious.”

Among the documents handed over to Mr. Flynn’s lawyers was an email talking about whether agents needed to warn the national security adviser that lying to the F.B.I. was a crime. Another email described the questions that agents should be prepared to answer if Mr. Flynn asked them.

Mr. Priestap did not immediately respond to an email requesting comment.

Mr. Flynn’s lawyers told Judge Sullivan last week after receiving the materials that there was little doubt what they proved: that Mr. Flynn had been deliberately set up by corrupt F.B.I. officials.

“Since August 2016 at the latest, partisan F.B.I. and D.O.J. leaders conspired to destroy Mr. Flynn,” the lawyers wrote to the judge. “These documents show in their own handwriting and emails that they intended either to create an offense they could prosecute or at least get him fired.”