Patenaude cited personal reasons when she submitted her resignation on Dec. 17.

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“It’s a bittersweet farewell to HUD,” Patenaude said in an interview.

She denied that internal conflicts played a role and said she looks forward to spending time with her husband at their home in New Hampshire. “These jobs are all-consuming,” she said. “There are no ulterior motives. I’m not mad at the administration.”

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Patenaude was the main administrator running the agency for much of her 16 months as deputy secretary, according to political and career HUD staffers.

She is departing at a critical moment for HUD, as its largely inexperienced political ranks grapple with the fallout of a prolonged partial government shutdown.

Her impending departure, planned before the shutdown began Dec. 22, hurt the agency’s ability to anticipate and plan for the closure, according to career and political staffers. HUD is under fire for not renewing hundreds of expired affordable-housing contracts before the shutdown went into effect, jeopardizing the budgets of property owners and the housing stability of low-income tenants.

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Housing advocates and HUD employees described Patenaude’s departure as a blow to an agency in which the morale of career staffers has deteriorated under Carson.

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“She knows the HUD building, the issues, the policies and the politics. She was an especially strong and important counterpoint to Secretary Carson’s early lack of knowledge on any of the issues that he was expected to lead on,” said Diane Yentel, president and chief executive of the National Low Income Housing Coalition. “When she battled some of the more ideologically far-right members of her administration, she typically won.”

Patenaude’s departure reflects a broader pattern of political appointees with expertise who are leaving the administration.

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Her confidants say there was not one blowup that precipitated her resignation but rather a series of incidents that left her feeling frustrated. The former HUD employee, who spoke on the condition of anonymity so as not to damage working relationships with the agency, characterized Patenaude’s job as “pushing this rock uphill over and over again only to have it fall back down.”

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Patenaude disagreed with the agency’s handling of an Obama-era fair-housing rule requiring communities receiving federal funds to address long-standing patterns of racial segregation, according to three people with direct knowledge of internal HUD debates. Carson had suspended the 2015 rule, calling it “burdensome.”

Patenaude told The Washington Post she did not support the rule as written by the Obama administration but said she wanted to educate communities about the law as the agency deliberated on a path forward. She said policy discussions continue.

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“My position was we had a moral and legal obligation to get it right,” Patenaude said. “Policy discussions are a series of explorations, and Secretary Carson and I are absolutely aligned on the need to educate America about fair housing.”

Patenaude had palm-size cards made listing the classes protected from housing discrimination — factoring race, color, religion, national origin, gender, disability and familial status — and distributed them widely. One agency official said Patenaude hoped the effort would help allay concerns of career employees and advocates that Carson’s team does not care about civil rights.

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Last fall, Patenaude expressed concern over the Trump administration’s intervention in disaster-recovery money that Congress had appropriated for Puerto Rico and states hit by hurricanes.

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President Trump in late September grew incensed after hearing, erroneously, that Puerto Rico was using the emergency money to pay off its debt, according to two people with direct knowledge of Trump’s thinking.

Trump told then-White House Chief of Staff John F. Kelly and then-Office of Management and Budget Director Mick Mulvaney that he did not want a single dollar going to Puerto Rico, because he thought the island was misusing the money and taking advantage of the government, according to a person with direct knowledge of the discussions who spoke on the condition of anonymity to describe sensitive internal deliberations. Instead, he wanted more of the money to go to Texas and Florida, the person said.

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“POTUS was not consolable about this,” the person said.

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Patenaude told White House budget officials during an early December meeting in the Situation Room that the money had been appropriated by Congress and must be sent, according to two people with direct knowledge of the meeting. She assured them that HUD had proper oversight of the funds.

Patenaude, who had visited Puerto Rico more than half a dozen times during her tenure, was about to make her final trip to the island as deputy secretary and wanted to ensure that Mulvaney’s team corrected any misinformation transmitted to the president, said a HUD official who was not authorized to speak on the record.

Patenaude told The Post: “I didn’t push back. I advocated for Puerto Rico and assured the White House that Puerto Rico had sufficient financial controls in place and had put together a thoughtful housing and economic development recovery plan.”

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In her meetings with Puerto Rico’s governor and other officials, Patenaude made it clear the territory would need to establish an oversight structure and meet other conditions to receive federal funding, said Carlos Mercader, the executive director of the Puerto Rico Federal Affairs Administration in Washington.

“Pam Patenaude showed the most commitment to Puerto Rico of any of the public officials inside the Trump administration,” said Mercader, who accompanied Patenaude on several of her visits to the island. “From the governor down, we are all grateful for everything she did.”

The week before Patenaude resigned, the U.S. territory received authorization to request future drawdowns for their long-term recovery efforts, including the development of affordable housing.

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“She didn’t want to abandon Puerto Rico,” said the HUD official. “Once she felt like she left Puerto Rico in a good place, she felt like she could leave.”

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The partial government shutdown has delayed Puerto Rico’s ability to access the first $1.5 billion of its nearly $20 billion in HUD disaster-relief funds.

Patenaude is the third senior political appointee with housing experience to leave HUD in recent weeks. Neal Rackleff, the assistant secretary of community planning and development, left in December. Michael Bright, executive vice president and chief operations officer at the Government National Mortgage Association, or Ginnie Mae, announced his resignation last week.

Patenaude, who began her career at HUD as a 21-year-old intern during the Reagan administration, has spent more than two decades in housing policy and economic development, serving as President George W. Bush’s assistant secretary for community planning and development at HUD.

“I’m going to continue to be supportive of the president and his agenda,” she said. “I’m going to be working very hard for his reelection.”