For weeks, Johns was caught in a protracted standoff between President Trump and congressional Democrats over whether the next federal budget should include billions of dollars for Trump’s proposed border wall. On Friday, Trump was set to sign a short-term budget deal that would reopen the government until Feb. 15, without the border wall funding he had demanded.

And as workers like Johns hope to return to their jobs, they are coming to terms with the reality that once-stable federal contract jobs can come and go at the whim of political forces beyond their control.

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“I don’t know why they keep doing this,” Johns said. “They just keep arguing with each other. And that’s not right, because a lot of people are out of work.”

Unlike federal workers, contractors are unlikely to receive back pay to make up for lost income. There is no guarantee that they will be able to return to work at all, with managers making such determinations on a case-by-case basis.

Johns is among thousands of people who benefit from a federal contracting set-aside program that employs disabled workers. Many were sent home without pay because of the partial government shutdown, nonprofit managers who employed them say, raising concerns about how the shutdown has hurt those least prepared to weather it.

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The people affected include those with “significant disabilities,” including learning disorders, who may have trouble coping with the anxiety of losing a job. With many of them already living paycheck to paycheck, some have fallen behind on bills. Others say they may have to stop paying for medications they need.

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The nonprofit government contractors that employ them operate in almost every state, highlighting how the shutdown has altered lives across the country.

Workers, managers and advocates worry that the extended shutdown threatened a federal program called AbilityOne, which designates certain federal contracts for nonprofits employing people who are blind or have other disabilities.

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John Kelly, vice president of government relations and public policy at SourceAmerica, an organization that works with more than 400 such nonprofits, said he is aware of 143 nonprofits across 43 states that were affected.

“We have more than 2,000 people with disabilities that were working on federal contracts that aren’t today,” Kelly said last week, when the shutdown stretched into its fifth week. “These are people who may have searched for this job for years, it really works for them and is a really key part of their life. And now they don’t know if they’re going to get that job back or not.”

The nonprofits affected include Chimes District of Columbia, an AbilityOne contractor that employs about 1,300 people, roughly 900 of whom report having a disability. Chimes executives reported sending 100 workers home without pay because of the shutdown. Work Inc., a contractor based in Dorchester, Mass., reported sending 29 people home without pay.

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Some, like Johns, saw their hours reduced or shouldered inordinate workloads as agencies tried to function with fewer employees.

Not all of those employed through the AbilityOne program are disabled. Under federal law, a nonprofit must devote 75 percent of its labor hours for a particular contract to “blind or other severely disabled individuals” to qualify for the federal program.

Those employed on AbilityOne contracts include veterans injured in combat; aging workers with diseases including Parkinson’s; those with developmental disabilities; the blind; and people who aren’t disabled. Their responsibilities include shoveling snow in front of government buildings and inspecting military vehicles. Some are skilled tradespeople who can find other employment, but many others depend on AbilityOne contract jobs for their livelihoods.

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The biggest AbilityOne customer, the Defense Department, did not lose funding during the shutdown. But a significant number of these employees work at civilian federal agencies, including the Interior Department, Commerce Department and the Environmental Protection Agency, where significant functions are deemed “nonessential” when the government shuts down.

Officials from the Trump administration and affected agencies said they were doing everything they could within the law to protect the jobs of contract workers.

“At the direction of the president, the administration is doing everything to make the lapse as painless as possible, consistent with law, and we urge Congress to do their jobs and quickly pass an appropriations bill that both opens the government and secures our borders,” said a senior administration official who spoke on the condition of anonymity last week to discuss the administration’s internal deliberations.

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Brian Hoey, a spokesman for the U.S. AbilityOne Commission, an independent federal agency that administers the program, said it was “closely monitoring” the shutdown’s impact. An Interior Department spokeswoman, Faith Vander Voort, said agencies are “taking all appropriate measures” to assist contract employees during the shutdown. Other agencies referred questions to the Office of Management and Budget.

“In complete compliance with all applicable laws, rules, and regulations, [Interior Department] Acting Secretary [David] Bernhardt is taking all appropriate measures to allow employees to work and earn a paycheck on time,” Vander Voort said in an email. “That applies not only to our full-time and part-time employees, but also to those that support us through contracts. We sympathize with folks who are experiencing difficult circumstances because Congress is failing to pass a budget that secures our borders.”

For the nonprofits that depend on AbilityOne contracts, the shutdown stretched finances thin. New contract awards all but ground to a halt at civilian agencies, making it hard to find new funding.

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Some managers kept their employees on the payroll through the shutdown by dipping into overhead, but it is unclear how long they would have been able to do so.

Jim Cassetta, president and chief executive of Work Inc., says he was forced to send 29 people home without pay who had been working at an EPA building and the federally funded John F. Kennedy Presidential Library, both in Boston. Many of them have been out of work since Dec. 22, while others are using up vacation and sick days.

Cassetta says the shutdown was a “double whammy” for disabled workers because it is hard for them to quickly find part-time work. Soon after news of the shutdown broke, he started rushing the workers to local unemployment offices to begin the process of getting them unemployment benefits.

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“Once they’re trained to do the job, they do phenomenal work,” Cassetta said of his disabled employees. “But they need to be supported; they need to deal with the anxiety of losing one job and being trained for another.”

One of those sent home from Work Inc. was Zach Weiner, who described himself as disabled. He was waiting for his unemployment benefits to kick in for his job in the mailroom of an EPA building.

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Another was Yolanda Pagan, a janitor at the JFK Library for two years under contract with Work Inc. She hadn’t worked since before Christmas and said she wasn’t able to pay all of her bills for January.

She said she has a learning disability that could make it hard to find another manager who would work with her.

“It’s not easy for me to just go anywhere and get a new job,” she said.

Another was Ray Garcia, an electrician who helps maintain the JFK Library under a contract with Work Inc. and who said he qualifies as a disabled person. Garcia says Work Inc. was able to pay him during the shutdown by letting him use vacation days.

“What I’m doing is I’m using up my vacation time, and then I’ll use the sick time,” Garcia said. “Once I run out of sick time, I’ve got nothing. I have enough to live for a couple of weeks and stuff . . . but soon I’ll run out.”

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Jacqueline Dailey has worked as a clerk at the Interior Department in Washington for the past two years under a contract with Chimes. Dailey said she had been unable to work since Dec. 24 and had to delay a medical procedure because her health insurance lapsed.