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The Justice Department declined to comment.

The intervention has contributed a turbulent period for the prosecutors’ office that oversees the seat of the federal government and some of the most politically sensitive investigations and cases — some involving President Trump’s friends and allies, and some his critics and adversaries.

This week, four line prosecutors quit the case against Roger Stone Jr., Mr. Trump’s close adviser, after Mr. Barr overruled their recommendation that a judge sentence him within sentencing guidelines. Mr. Barr’s intervention was preceded by criticism of the original sentencing recommendation by Mr. Trump and praised by him afterward, and Mr. Barr on Thursday publicly asked Mr. Trump to stop commenting about the Justice Department.

The moves amounted to imposing a secondary layer of monitoring and control over what career prosecutors have been doing in the Washington office. They are part of a broader turmoil in that office coinciding with Mr. Barr’s recent installation of a close aide, Timothy Shea, as interim United States attorney in the District of Columbia, after Mr. Barr maneuvered out the Senate-confirmed former top prosecutor in the office, Jessie K. Liu.

Mr. Flynn’s case was first brought by the special counsel’s office, who agreed to a plea deal on a charge of lying to investigators in exchange for his cooperation, before the Washington office took over the case when the special counsel shut down after concluding its investigation into Russia’s election interference.

Mr. Flynn’s case has been bogged down in recent months by his lawyers’ unfounded claims of prosecutorial misconduct; a judge has already rejected those accusations. Mr. Flynn then asked to withdraw his guilty plea, which he first entered in December 2017. His case has become a cause célèbre for Mr. Trump’s supporters.