After Environmental Protection Agency Administrator Scott Pruitt returned from a trip to Italy last summer, a newly hired scheduler at the agency was asked to remove a particular name from his calendar: Cardinal George Pell, who had dined with Pruitt in Rome and later was charged with sexual misconduct.

Madeline Morris objected to that request and other deletions to the EPA chief’s calendar, which she believed could be illegal under federal rules, according to two individuals who spoke on the condition of anonymity to discuss internal agency deliberations. Not long after pushing back against the practice, Morris was dismissed after barely three months on the job.

She received severance pay for a month and a half after leaving the agency, an arrangement documented in emails released recently under a Freedom of Information Act lawsuit filed by the Sierra Club, an environmental advocacy group. However, federal employment law experts said such severance payments are not permissible.

EPA officials said that while they were limited in what they could say about Morris’s dismissal, it was not out of retaliation.

Reached on Wednesday by phone, Morris declined to comment.

The New York Times first reported Morris’s objections, and her subsequent dismissal, on Thursday afternoon.

Pruitt, who had become the focus of more than a dozen federal probes about his spending and management decisions, resigned later Thursday.

EPA officials said Thursday that although they made changes to Pruitt’s schedule after the fact, those alterations were typically made within a matter of days and aimed to reflect what the administrator ended up doing and who participated in those events. They disputed recent statements by Kevin Chmielewski, Pruitt’s former deputy chief of staff for operations, that the administrator kept a “secret” calendar and that his aides would purge certain events from his public one.

“Despite continued false accusations, there are no secret calendars or schedules,” EPA spokesman Jahan Wilcox said. “EPA has released the meetings and events Administrator Pruitt has attended — which the media has already reported as meetings with industry — and to report anything else would be categorically false.”

Early in June 2017, Morris seemed eager to join the EPA to work for Pruitt .

“Thank you so much! I am so excited for this opportunity and can’t wait to join the team,” she wrote on June 6, 2017, to Pruitt’s chief of staff, Ryan Jackson. She told him that she had given notice at her job as a federal affairs specialist for the Koch brothers — a position she had held since December 2012.

Morris, who worked as a scheduler for former Rep. Denny Rehberg (R-Mont.) as well as for Koch Industries, left the EPA by mid-September — three months after she started — but was still receiving a paycheck.

“Hi Ryan. I hope all is well over at EPA,” Morris wrote on Sept. 22, 2017, from what appears to be a personal email address. “I just wanted to check in with you. I am working with some headhunters, and they would prefer if I had a reference at my last place of employment. Would you feel comfortable doing that? Also, I haven’t gotten paid yet. I usually get paid on Thursday. I wanted to see if something has changed since our conversation about being paid a few months.”

Jackson soon replied: “Let me know if it doesn’t come through by Tuesday. That’s apparently the pay date for this pay period. We have not put in any paperwork on you so no one is aware of any actions.”

Four days later, on Sept. 26, Morris wrote back: “Hi Ryan, sorry to bother you. I still haven’t received my paycheck. Let me know if you would like me to do something on my end.”

“It’s not a bother. I’ll get on this,” Jackson replied.

Joseph Kaplan, who teaches in American University’s Department of Public Administration and Policy, said in an email that such payments would not comport with federal guidelines.

“I have never heard of severance pay to a federal employee outside of settlement of a legal claim, or as part of an [Office of Personnel Management] approved early retirement incentive,” Kaplan said.

Morris was not the only EPA employee to voice concern about changes to Pruitt’s official schedule. Three current and former EPA officials said in interviews this week that Pruitt did not keep a secret calendar, but that he and his aides exercised considerable discretion in what information they decided to disclose as part of the public calendar that has been released through Freedom of Information Act requests.

For example, Pruitt himself would determine which attendees needed to be disclosed when it came to meals that he had with different people if they did not have direct business before the EPA. In Pell’s case, for example, Pruitt and his aides determined after the fact that because it was a dinner, the agency did not need to disclose who participated in the June 9 meal at La Terrazza, a high-end restaurant. It’s not clear when Pell’s name was removed from the calendar.

Pell — who denies any criminal wrongdoing — was charged with sexual assault three weeks after the dinner Pruitt and his aides had in Rome with several high-ranking Vatican officials, which was arranged by then-Federalist Society executive vice president Leonard Leo. Pell’s presence first became public after an email from Pruitt’s former policy adviser Samantha Dravis was released through a FOIA request by the advocacy group Natural Resources Defense Council, and documented in subsequent FOIA requests by the Sierra Club, another environmental organization.

A senior EPA official, who spoke on the condition of anonymity to discuss internal deliberations, confirmed that aides made the decision to not name Pell but added that they also omitted references to a dinner the administrator and his staff had with a former top aide to Pope Benedict XVI during that same trip.

“We put together the schedule but even when we were over there, the schedule would change,” the official said, adding, “Especially when we got back, we scrubbed it” to ensure that it was accurate.

Chmielewski, for his part, has said in multiple interviews that Pruitt and his top aides declined to identify certain meetings that they viewed as politically embarrassing.

In an interview Tuesday on MSNBC’s “All In With Chris Hayes,” Chmielewski said that the administrator would travel “and the next thing you know we would be asked to basically scrub things that he did that would be controversial. Cardinal Pell being one of them and there were some other trips.”

On Thursday two Democratic House members, Don Beyer (Va.) and Ted Lieu (Calif.) asked the EPA’s Office of Inspector General to review whether Pruitt violated the Federal Records Act in altering his calendar.

“We ask that you protect that public trust, and establish whether Administrator Scott Pruitt violated the Federal Records Act, and if so, determine what he concealed and why,” they wrote. “Further, we ask that you take the appropriate steps to hold him accountable for such actions, as required by law.”

Alex Howard, an open government advocate, said in an interview that the omissions in Pruitt’s calendar speaks to the wide latitude Cabinet officials have when it comes to public disclosure.

“There’s tremendous discretion given to each agency to decide what’s put up, and to decide what’s exempted or not,” Howard said, adding that the fact that new details have emerged through FOIA litigation “means the government’s spending a bunch of money to try to fight disclosure for something that should just be put online.”