By Jeremy Herb, Tami Luhby, Sunlen Serfaty, René Marsh, Alexandra Skores, Ella Nilsen, Marshall C

(CNN) — The government shutdown is over. But hundreds of thousands of federal workers are coming back after 43 days to anything but normalcy, employees from across the country told CNN.

Flight delays and cancellations will linger as Air Traffic Controllers staff back up. Workers who haven’t received a paycheck in weeks will still have to wait for back pay. Research grants will be delayed. Economic reports are likely to be scrapped. Six weeks of email and voicemails will have to be waded through.

And in three months, they may have to contend with turbulence all over again: The agreement President Donald Trump signed into law Wednesday evening funds most of the government only through January.

“There’s no back to normal in this deal because all it does it kick the can until January 30,” said Max Stier, president and CEO of Partnership for Public Service, a nonpartisan nonprofit government organization.

“It’s a little like the federal workforce is going to return to their house after a hurricane and there’s another storm on the horizon.”

Federal workers said that the shutdown has been an exclamation point on top of months of chaos as the Trump administration has slashed jobs and, in some cases, entire agencies since the president took office in January. The administration sought to fire more federal workers when the shutdown hit, but the short-term funding deal halted those dismissals until the end of January.

“It’s going to be stressful for everybody,” said Yolanda Jacobs, president of the American Federation of Government Employees Local 2883 and a Centers for Disease Control and Prevention employee. “We can only begin to imagine how difficult it’s going to be get everything functioning again, especially since we were already limping along in a lot of ways before the shutdown happened.”

For the American public, the lingering effects of the shutdown could be felt for months or even years to come at the nation’s airports. Meanwhile, those receiving government assistance like food stamps are eagerly awaiting the government to finally get funds out the door.

A slew of backlogs

Federal workers back on the clock Thursday will need to assess how to address more than six weeks of backlogs. Federal employees not deemed essential were furloughed throughout the shutdown.

From food safety and NASA to education and the national parks, federal workforces were already short-staffed following widespread cuts from DOGE earlier this year, which employees told CNN will make it even harder to dig out from the under the shutdown.

“This moment is going to look very different than in 2019 (after the last government shutdown) when these offices were fully staffed,” said an Education Department employee.

A second Education employee told CNN that they were told only check their emails at approved times to look for “reduction in force” layoff notices — and to make sure their computers didn’t lock down after 30 days.

It was “heart wrenching” to see the emails piling up, the person said, including with desperate pleas from parents of disabled children who filed discrimination cases with the department’s Office for Civil Rights. Another Education official estimated that, during the shutdown, there were more than 2,000 complaints filed with the office, which handles allegations of discrimination against students with disabilities.

It will take days to get labs used to test food and prevent food-borne illnesses at the Food and Drug Administration back to full capacity at the agency’s testing labs, said one worker at the agency’s Human Foods Program.

Besides having to catch up on equipment maintenance and quality checks, “it will take time to restart research along with broader policy planning,” the worker said.

And at the Internal Revenue Service, backlogs in tax filings from those who filed for extensions will take “two to three months to catch up,” said Gibson Jones, president of the National Treasury Employees Union Local 98 in Memphis. “You’re talking about more than 40 days of mail that no one touched. People who are expecting money back will also see a delay in processing those tax refunds.”

A big focus at the National Park Service will be assessing any damage that occurred to parks during the shutdown, said Kristen Brengel, senior vice president of government affairs at the National Parks Conservation Association.

Many parks had law enforcement staffing during the shutdown, but there have been reports of graffiti and off-road vehicle damage in parks like Arches and Glen Canyon, as well as reports of illegal activities like base-jumping and flying drones in Yosemite, Brengel said. But there was a surge of volunteer support during the shutdown, she said, and many parks paid for custodial services like garbage removal with fee money — or volunteer groups stepped in to help.

“Thankfully, many parks didn’t get damaged,” Brengel said. “But this is unsustainable and everyone knows it.”

At NASA’s iconic Goddard Space Flight Center’s main campus in Greenbelt, Maryland - home of the Hubble and James Webb space telescopes - employees were alarmed as more than a dozen buildings on the campus were emptied and padlocked, with very little notice given, CNN recently reported.

Some of the sources CNN recently spoke to said they fear the sudden moves are part of an effort by the Trump administration to quietly gut the Goddard campus during the shutdown — a claim a NASA spokesperson denied.

“There will be many people who have no idea that this facility closure situation is going on,” a NASA engineer said. “I expect that will be a pretty crazy situation on top of just coming back.”

When will employees receive back pay?

When the roughly 1.4 million federal workers who have been furloughed or working without pay will receive their back pay may vary by agency. Many have missed two full paychecks and a partial one during the shutdown.

In the past, it only took a few business days for workers to be paid, said Jacqueline Simon, policy director at the American Federation of Government Employees. But she was concerned that this year it could take longer because many human resources staffers at agencies were furloughed or have left amid the administration’s downsizing efforts.

Adding to the complexity is that federal workers are not all paid at the same time since the government uses multiple pay systems, said Stier of Partnership for Public Service.

“It’s a huge undertaking on top of a lot of other things that the federal employees are going to have to be doing,” he said, though it should take a matter of days, not weeks.

But “until we get paid, everyone’s going to still have those same financial stressors on them,” said Ben Emmel, who represents 2,400 Government Accountability Office employees as president of the International Federation of Professional & Technical Engineers Local 1921.

Effects on air travel could linger for years

The shutdown brought chaos to US airports, and the impact could linger well beyond the reopening of the government.

The US air traffic control system is more than 3,000 controllers short of what’s needed to fully staff towers and other facilities that guide planes throughout the country. The current workforce of 14,000 controllers not only had to deal with the regular staffing shortages but also more coworkers not showing up during the shutdown, all while not getting paid.

All this put young controllers in a “very difficult position” during the shutdown, leading some to quit, Transportation Secretary Sean Duffy told reporters this week, while some older controllers chose to simply retire.

Fifteen to 20 retirement-aged controllers have left per day, Duffy said, up from four in a typical day.

In May, the Department of Transportation said it would replace the decades-old Federal Aviation Administration infrastructure with a new air traffic control system for $31.5 billion, but the shutdown could hurt that effort as well.

At a Wednesday press conference at Chicago’s O’Hare International Airport, Duffy said the software and upgrades the new system requires “would take longer than the three-year period,” originally promised.

When will safety net programs be funded?

The shutdown wreaked havoc on the nation’s safety net programs, most notably food stamps relied upon by nearly 42 million Americans to feed themselves and their families.

Just when enrollees in the Supplemental Nutrition Assistance Program, or SNAP, will receive their full benefits for November will depend on where they live. More than a dozen states started issuing full allotments to residents last week before the Supreme Court paused a court order requiring full funding for the program. Several other states began sending partial benefits last week based on an earlier court order. Other states have not yet distributed any of this month’s aid.

After the government reopens, many states could issue full SNAP benefits within three days, said Lexie Kuznick, director of policy and government relations for the American Public Human Services Association, which represents state, county and city agencies. Some, however, could take up to a week to do so.

The spending agreement signed into law takes the threat of another lapse of SNAP off the table in January when another shutdown could occur: The bill funded several agencies, including the US Department of Agriculture, which administers SNAP, for the entire fiscal year.

However, the Low Income Home Energy Assistance Program, or LIHEAP, and Head Start could take longer to restart. They are run by the Department of Health and Human Services.

It typically takes at least 30 days for the HHS to calculate states’ allocations and get the money out the door for LIHEAP, said Mark Wolfe, executive director of the National Energy Assistance Directors Association. And he fears it will take even longer this year since HHS laid off its LIHEAP staff in the spring.

Federal grants for the roughly 140 Head Start programs – serving more than 65,000 children and families – that were affected by the shutdown could take up to two weeks to distribute, said Tommy Sheridan, deputy director at the National Head Start Association.

The funding lapse forced 20 programs in 17 states and Puerto Rico to close. Other programs have been able to maintain their operations thanks for local and philanthropic support.

Asked about the timeline for getting funds to LIHEAP and Head Start programs, an HHS spokesperson said that the agency will “work swiftly” to administer LIHEAP annual awards. Head Start recipients can expect to receive communications that will include a timeline for the release of federal funds.

Economics reports delayed

Economic data released by the government — which is used by business leaders and the Federal Reserve to assess the state of the US economy — has been suspended throughout the shutdown.

Monthly employment reports for September and October haven’t been released, and neither has the first estimate of third-quarter gross domestic product, which captures all the goods and services produced in the economy.

Once the government reopens, statistical agencies such as the Bureau of Labor Statistics and the Bureau of Economic Analysis will release updated schedules on data releases.

But this is the first time there have been two delayed jobs reports. And it’s likely that October’s report will never be released, as data for the month was not collected, White House Press Secretary Karoline Leavitt said Wednesday.

“All of that economic data released will be permanently impaired, leaving our policymakers at the Fed flying blind at a critical period,” Leavitt told reporters.

Headed for the exit?

Caitlin Lewis, who runs CivicMatch, which connects federal employees with jobs in state or local governments, said the shutdown has pushed many federal workers to the exits.

There was a 74% spike in federal workers signing up for the platform during the first five weeks of the shutdown, she said, compared to the five weeks before the shutdown. Last week was one of the platform’s busiest weeks in months.

Overall, more than 12,000 federal employees have signed up this year.

“People want to stick it out as long as they can. But this is the latest in a deep cycle of instability that is pushing public servants out of the government since the inauguration,” Lewis said.

When the last government shutdown ended in 2019, a USDA employee returned to find dozens of emails from state agencies with policy questions, which gave her a newfound appreciation for her work and how much she is needed.

But the stress of this year’s record-long impasse has forced her to start looking for other jobs.

“This has been the worst six weeks that I can remember,” said the staffer, who had planned a career with the government. “I cannot afford to go through this again, mentally or financially.”

The-CNN-Wire
™ & © 2025 Cable News Network, Inc., a Warner Bros. Discovery Company. All rights reserved.