U.S. District Judge James Boasberg again ordered government lawyers to answer his questions and said they should do so in a sealed filing by noon Wednesday.
The Department of Homeland Security issued Khalil a notice to appear before an immigration judge for deportation proceedings, with a hearing set for March 27 in Louisiana.
The judge, who reinstated Gwynne Wilcox to the National Labor Relations Board, said Trump's "power to remove federal officers and honest civil servants ... is not absolute."
The federal judge called the Department of Government Efficiency's work "opaque" as he ordered an official to shed more light on its activity and structure.
The Justice Department ordered the charges be dismissed on Feb. 10, prompting resignations of prosecutors and allegations of "quid pro quo" with the Trump administration.