At a court hearing Thursday, U.S. District Judge Nicholas Garaufis questioned New York state officials and disability advocates about people with mental illness dying or coming to harm after moving from adult group homes into “supported housing” apartments, problems raised in a ProPublica and Frontline investigation published that day with The New York Times.

He ordered an independent report to assess the effectiveness of the state’s incident reporting system, got the state to commit to examining its service-coordination program and suggested the state develop a program to help residents learn and practice basic life skills in supported housing.

Four years ago, in a landmark settlement secured by advocates, Garaufis issued a court order offering more than 4,000 adult home residents in New York City a chance to move. The idea was that many did not need to live in such facilities — which can house hundreds of residents and have a history of abuse and neglect — and could instead thrive in their own apartments with the right support. The order instructed evaluators to presume that all residents would be fit to do so.

But ProPublica and Frontline found that clinicians evaluating adult home residents for the transition felt censored when they raised concerns about a person’s ability to live alone, and that workers felt pressured to “sell the move,” even to people who they thought were ill-equipped.

We found that more than two dozen people who left the adult homes were not able to care for themselves, ending up in unsafe or inhumane living conditions. We identified six deaths that raised questions about whether people are being moved despite concerns about their ability to live alone, and whether social service agencies and the state are doing enough to intervene once problems emerge. One man died of liver failure after repeated warning signs about his drinking problem; another died naked inside the foyer of his building during a blizzard, days after neighbors had seen him “practicing his karate” in the snow.

The state has declined to give details about its death investigations, saying they are shielded by state law.

At the hearing, which had been scheduled before the story was published, Garaufis expressed concern that some people are not getting the help they were promised and that the government is failing to track and address problems.

“This case has never been about relocating people. This case is about improving the quality of life for people with serious mental illness,” he said. “This is not about numbers as much as it is about achieving that goal.”

In court, Garaufis said the state and advocates needed to ensure that those granted the opportunity to leave were indeed able to “handle it.”

The judge asked whether the state and its service contractors are doing enough to curb problems that can become dangerous over time.

“What has been done … to intervene in situations before they become dire?” Garaufis asked.

As ProPublica and Frontline reported, the state only recently developed a system to track deaths and other adverse outcomes for former adult home residents living in apartments.

In court Thursday, Clarence Sundram, the independent monitor installed to oversee the transition, said the new system represents an improvement, but the state still is not providing enough detail on why incidents occurred or how they could have been avoided.

The judge asked Sundram to deliver a report assessing the system by Jan. 31. “I’d like to get a better sense of how you’re doing in this area,” he told state officials.

He asked about a program called Adult Home Plus, which the state instituted in 2015 to give supported housing residents more intensive social services and a worker to coordinate care. ProPublica and Frontline found that coordination among those teams sometimes suffers from poor communication and confusion over responsibilities, leaving workers and patients at risk.

Garaufis said he was worried now that the program was “not broad enough to address persistent problems.”

In response to his questions, Lisa Ullman, who leads the effort to implement the settlement for the Department of Health and Office of Mental Health, promised to examine the program. She said she recognized it was “extremely important that we do what we can to support people once they are in supported housing.”

State officials have said that most residents succeed in supported housing, and have been appropriately placed after thorough assessments.

Disability rights attorney Cliff Zucker, who filed the lawsuit that led to the landmark settlement, said he expected a rigorous analysis of problems and shared concerns with the judge and the state about what he called a “small number” of people who failed. He also noted that the yearly state stipend for rent and other services is set to increase from roughly $17,000 to $20,000 for supported housing residents, which he said would help them find better apartments and afford them more help. The advocates also mentioned that they had previously pushed the state to offer supported housing residents more services and better oversight.

In a statement, Jota Borgmann, an attorney for Mobilization for Justice, said “we are always deeply concerned when we learn of class members who are in peril or who have died, whether they have moved out into the community or remain in adult homes.”

She also pointed out that people continue to die in the adult homes. She sent figures she said she received from the state that suggest the death rate appears to be roughly twice what ProPublica and Frontline reported as the rate of death in supported housing.

At the hearing, Garaufis also heard updates on continued delays in assessing and moving people out of adult homes, as well as court challenges from adult homes arguing that people with mental illness should still be allowed to move into them.