The government shutdown closes offices, museums and other sites in Washington, D.C. File photo from 2013. Photo by Diego M. Radzinschi/NLJ

The Trump administration's agreement Friday to temporarily fund the government for three weeks, ending a record-breaking shutdown, creates fresh uncertainty for the courts, federal agency lawyers and private attorneys who have grappled with delayed litigation for more than a month now.

The U.S. Justice Department had asked federal trial and appellate courts across the country to pause thousands of civil cases over the past month, amid the lapse in federal appropriations that has left hundreds of thousands of federal workers furloughed without pay.

The government's lawyers had mixed success. Some judges spurned the government's requests, while others paused cases until funding is restored. In their stay requests, Justice Department lawyers said they would alert the court when the government reopens.

Justice Department lawyers will file those notices with the possibility that the government will shut down once again in a few weeks. Government lawyers could, in theory, ask courts to leave their stays in place.

“My guess is that government lawyers and the courts will proceed as though this were a long-term deal,” said Sasha Samberg-Champion, counsel at Relman, Dane & Colfax and a former lawyer in the DOJ's Civil Rights Division. He added: “I don't think there's much basis for the courts not to resume cases so long as there's funding, or for the DOJ not to litigate them.”

In his remarks Friday, President Donald Trump signaled that another shutdown could come in mid-February.

“If we don't get a fair deal from Congress, the government will either shut down on February 15th, again, or I will use the powers afforded to me under the laws and the Constitution of the United States to address this emergency,” Trump said Friday.

Federal rules prevent most government employees from working during shutdowns. In the event of a shutdown next month, government lawyers will likely require fresh orders rejecting stay requests to continue litigating cases.

“They may have to go through the practical issue of asking for another stay, then waiting a few days and being in limbo before they're able to work,” said Steptoe & Johnson LLP partner Markham Erickson, who successfully resisted the government's request to delay arguments in a challenge to the Federal Communications Commission's decision to repeal the so-called net neutrality regulation. “They have to put their pens down until they get an order from the court saying, 'No, you will proceed.' It has a very disruptive impact. At the moment the government shuts down again, the pens have to go down for some of the lawyers.”

The Justice Department, as of Friday afternoon, has not said how it plans to proceed. A department spokeswoman declined to comment.

The agency's requests could affect a number of high-stakes cases. The U.S. Court of Appeals for the Fifth Circuit, for instance, obliged the DOJ's request to pause Affordable Care Act litigation.

But a number of judges have sternly rejected the government's request to pause cases amid the shutdown. In one particularly blistering rebuke, a Boston federal judge described lapses in government funding as “simply an abdication by the president and the Congress (which could override a presidential veto) of the duty to govern responsibly to the end that all the laws may be faithfully executed.”

“Nor does such a lapse in any way excuse this court from exercising its own Constitutional functions,” wrote U.S. District Judge William Young in an order denying a stay.

“A lapse in appropriations cannot delay or deny American jurors their constitutional right to adjudicate cases ready for trial,” Young added. “It cannot delay or deny other litigants their constitutional right to their day in federal court or any preliminary step necessary to get there.”

Young added: “Appropriation or no, this court will continue to sit daily, attending to the quotidien details of getting all cases ready for trial and trying them in a timely fashion as required by the Constitution.”

Any funding resolution that Congress passes and the president signs won't resolve the lawsuits from federal workers and federal labor unions that are seeking back pay and other damages resulting from Trump's shutdown. Indeed, workers are still fighting for certain payments from the last major shutdown, in 2013, which lasted more than 20 days.

Read more:

DC Circuit Judges Feud, and New Suits Pile Up, as Shutdown Persists

Some Federal Judges Spurn DOJ's Push to Pause Cases During Shutdown

Federal Employees Lose Early Bid to Stop Unpaid Work During Trump's Shutdown

Fifth Circuit Freezes Big Obamacare Case Amid Trump's Shutdown