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“I hope there are no more resignations,” Mr. Barr said. “We, we like our prosecutors and hope they stay.”

As Mr. Trump has pointed out on Twitter, two of those prosecutors — Aaron Zelinsky and Adam C. Jed — helped carry out the special counsel’s investigation, which Mr. Trump detested. Their supervisors reassured them this week that they would suffer no retaliation for withdrawing from the Stone case.

Timothy J. Shea, a close ally of Mr. Barr’s who took over this month as interim U.S. attorney for the District of Columbia, sent his staff an email of support this week. “While there are times where reasonable minds may disagree, I respect the work that each of you do, and I will do my best to support our work,” he wrote.

Mr. Shea’s role is especially fraught because the Washington office, the largest in the country with 300 lawyers, often handles politically sensitive cases and inherited several prosecutions begun under Mr. Mueller. At least some in that office privately complained that Mr. Trump and Mr. Barr both treated Mr. Shea’s predecessor, Jessie K. Liu, shabbily.

Ms. Liu, a Trump appointee, was viewed in the office as a leader who helped protect prosecutors from political meddling. But her relationship with other department officials grew strained, especially after she decided there was insufficient evidence to seek an indictment of Andrew G. McCabe, the former deputy director of the F.B.I. and a frequent target of the president, according to two people familiar with the situation.

She was nominated for a top job at the Treasury Department and transferred there this month to await her confirmation. Then this week, the president decided to rescind her nomination, even over Mr. Barr’s objections, according to three people familiar with the discussions.