Asked to explain Ms. Morris’s departure from the E.P.A., as well as his own email correspondence indicating that she was being paid for time not worked, Mr. Jackson declined to comment. He also declined to comment on whether Ms. Morris was simply being asked to reconcile calendars.

The E.P.A. spokesman and the agency’s general counsel declined to comment.

Ms. Morris had nearly a decade of experience in Washington and solid Republican credentials, according to her résumé. She worked for former Representative Denny Rehberg, a Montana Republican, as an assistant and scheduler, before working as a federal affairs specialist for Koch Companies Public Sector, the lobbying arm of Koch Industries, the conglomerate long run by the conservative brothers David H. and Charles Koch.

Ms. Morris, whose start date at the E.P.A. was June 18, was an executive scheduler with an annual salary of $90,350. She handled a variety of planning needs for Mr. Pruitt, including requests for meetings with executives from Toyota and Chevron.

The account of the calendar deletions and the aftermath is based on interviews with four people who were working at the agency at the time, including Mr. Chmielewski and three others who asked not to be identified out of concern for retaliation.

In July 2017, according to Mr. Chmielewski, Ms. Morris was instructed by him and Mr. Jackson to retroactively delete some meetings Mr. Pruitt held with lobbyists and replace them with staff meetings in the calendar, which was maintained in Microsoft Outlook. He and other people familiar with the calendar also said Ms. Morris was asked not to enter some of Mr. Pruitt’s meetings on the official calendar.

Mr. Chmielewski cited an August 2017 meeting with billionaire Denver-based businessman Philip Anschutz, a prominent donor to Republican Senate candidates and owner of an energy company regulated by the agency. Mr. Pruitt’s calendar for that day, which was publicly released, does not include the meeting.