The government has reopened. What’s that mean for air travel?

By Andy Rose, CNN

(CNN) — People flying home for Thanksgiving this month have their list of things to be thankful for: the turkey, football, time with family. This year, they can also add H.R. 5371 to the list.

That’s the funding bill President Donald Trump signed into law on Wednesday to reopen the government, ending the longest government shutdown in US history.

The move is a step closer to normalcy for flyers after cuts mandated by the Federal Aviation Administration led to thousands of flight delays and cancellations at major airports across the country.

“I think the system should return to normal by the weekend. I really do,” Delta Air Lines CEO Ed Bastian told “CBS Mornings” on Thursday.

“Thanksgiving is going to be a great holiday period of travel,” he added.

But before they get to say grace with family, travelers are now praying Bastian’s assessment is right, even as many questions remain about how quickly air traffic controller staffing will stabilize and when Transportation Security Administration workers will get paid.

Here is what we know about the plans to get more planes back up in the skies – and the uncertainty that remains.

When will airlines stop canceling flights?

The morning after the federal government reopened, Hartsfield-Jackson Atlanta International Airport was filled with travelers keeping the hectic pace typical of the world’s busiest airport. But a closer look revealed something new: a palpable sense of relief in travelers.

“I am happy that it will get back to some kind of normalcy or just a little bit better before the holidays,” Metreia White said, before boarding a flight to Fort Lauderdale, Florida.

Hartsfield-Jackson is one of 40 major airports where airlines are still under orders from the FAA to cut 6% of their flights, many on shorter regional routes. Transportation Secretary Sean Duffy said the cancellations have been necessary for safety because of air traffic controller staffing shortages during the shutdown.

Fridays and Saturdays have seen the most staffing problems throughout this time, according to data viewed by CNN.

Air traffic controllers missed two paychecks since the shutdown started on October 1, and some are taking second jobs to make ends meet or calling in sick in protest.

“This has all been data-based,” Duffy said, citing examples of airplane mishaps at a news conference at Chicago O’Hare International Airport. “We’ve seen heightened complaints by pilots of the communication they’re having with air traffic controllers.”

But “staffing levels … improved dramatically” when it became clear that a funding deal was coming, Bastian said.

“I think our air traffic controllers are seeing an end to the shutdown, and feel more hopeful, and they are coming in,” Duffy said on Tuesday. The Department of Transportation stopped short of the planned 10% cuts because more air traffic controllers started showing up at work.

They will remain frozen at 6% until the FAA determines it is safe to resume more flights.

Logistics can also impact flight schedules, according to Airlines for America, a trade group representing major US airlines.

“Airlines cannot flip a switch and resume normal operations immediately after a vote — there will be residual effects for days,” the group’s president and CEO, Chris Sununu, said in a statement this week.

“Canceling one flight has a domino effect. They’ve had to move different airplanes in untraditional ways,” Sununu added at a news conference on Wednesday.

Despite the challenges, airlines expect to rally quickly.

Delta Air Lines said in a statement Wednesday that it expects to be “back to full capacity over the next few days.”

Southwest said on Wednesday they’re “seeing real progress, and air travel appears to be returning to normal. Our operation remains strong, and Customers can continue to count on Southwest.”

American Airlines leaders told employees in a letter Thursday that they are optimistic about minimizing cancellations in time for the holiday.

“It may take a few days for fully normal controller operations to resume, and we may need to continue to reduce schedules to comply with the FAA’s emergency order requirements,” wrote CEO Robert Ison and Chief Operating Officer David Seymour. “But we have seen promising signs and are confident that because of our strategic planning and work to minimize customer impacts throughout this period, we will recover quickly and deliver a strong Thanksgiving operation.”

When do air traffic controllers get paid?

Homeland Security Secretary Kristi Noem said on Thursday her team finished up the administrative work necessary “late last night” so TSA employees could receive back pay for paychecks missed during the government shutdown as soon as possible.

“They’ve already missed pay periods and recognizing that that’s a hardship on their families,” Noem said. “So we did all of the administrative work that we needed to late last night to ensure that payroll would be processed as soon as possible, and within the next coming days, they will get that into their bank accounts.”

A DHS spokesperson told CNN the agency “will be working to expedite pay for all employees who were furloughed or working without pay in an excepted status.”

Noem also announced some TSA employees who “stepped up every single day” and “served with exemplary service” through the federal government shutdown would receive a $10,000 bonus check.

“They were all examples of what we need and we will be continuing to not only recognize employees across the country, but we will be looking at every single TSA official that helped serve during this government shutdown and do what we can to recognize that and help them financially with a bonus check to get them and their family back on their feet,” the secretary said.

Earlier this week, Duffy said that air traffic controllers were expected to get 70% of their back pay “anywhere from 24 to 48 hours after the government opens,” with the remainder to come a week later.

Technicians who work on air traffic control equipment are also awaiting their back pay, said David Spero, national president of their union, PASS National.

“I think this is going to take time,” said Spero. “We’re going to have people with ongoing pay issues for a while.”

He also said the technicians who continued to maintain air traffic control equipment through the shutdown deserve recognition, too.

“I’m looking into it and reaching out to FAA leadership now,” Spero said Thursday. “Not one delay in the last 43 days has been attributed to a system outage or an equipment problem.”

What are the long-term impacts on travel?

Major airlines have acknowledged losing millions of dollars of revenue from the canceled flights, and industry leaders said travelers were getting wary of putting money down on a trip that might not happen.

“The consumer is pulling back,” said Sununu. “Typically, airlines and hotels can be a leading indicator of where folks are spending their money in the economy.”

US domestic flights are expected to cost 6% more over Thanksgiving week this year compared to last and rise 7% during the year-end holiday period, according to discount air travel site Going.com, but it’s not clear how those prices were affected by the flight cuts.

One bit of ironic luck for both airlines and passengers in the midst of this misfortune, according to the Delta CEO, is that all major carriers were equally impacted, so the financial loss shouldn’t result in higher ticket prices.

“It’s a competitive marketplace,” said Bastian. “Everyone went through the same thing.”

The airline industry says in the future, the government should guarantee the stability of the air travel system, even in a shutdown.

“The FAA’s Airport and Airway Trust Fund currently has $5 billion that could be used to pay air traffic controllers during future shutdowns,” Airlines for America said in a statement. “We ask Congress to consider legislation that would implement a long-term solution.”

There are other impacts too, that won’t be solved by 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, 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.

Could this happen again in January?

The agreement Trump signed into law Wednesday evening funds most of the government only through January.

That means that airlines and passengers may be grounded again in three months.

“There’s no back to normal in this deal because all it does is 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.”

Geoff Freeman, president and CEO of the US Travel Association, said it takes time to rebuild – both operations and morale – after disruptions like this to the travel industry.

“America cannot afford another self-inflicted crisis that threatens the systems millions rely on every day,” said Freeman.

CNN’s Alexandra Skores, Aaron Cooper, Pete Muntean, Tami Luhby, Chris Boyette and Amanda Musa contributed to this report.

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