By Casey Gannon, Holmes Lybrand, Katelyn Polantz, CNN

(CNN) — A day after a federal judge dismissed indictments against former FBI Director James Comey and New York Attorney General Letitia James, federal prosecutors in Virginia are still in the dark on how to proceed with the tossed cases.

A judge decided Monday that interim US Attorney Lindsey Halligan didn’t have a prosecutor’s authority when she secured the grand jury indictments that President Donald Trump wanted of two political foes. Now, assistant US attorneys in her office are trying to do their jobs with little idea of who is in the driver’s seat — with no word yet on the Justice Department’s next moves in those high-profile cases against Comey and James, and little guidance on who’s in charge in the rest of the active criminal investigations out of the Eastern District of Virginia.

Federal Judge Cameron McGowan Currie dismissed both indictments after she found that Halligan’s appointment was unlawful.

Currie ruled Monday that all of Halligan’s actions following her “defective appointment” were “unlawful exercises of executive power and are hereby set aside.” Both Comey’s and James’ cases were tossed without prejudice, meaning the prosecutors could bring the same charges to a grand jury in an attempt to have them indicted again.

“There’s panic over what to do,” one person close to the Alexandria, Virginia, prosecutors’ office told CNN about making moves in criminal matters in the wake of Monday’s ruling.

Comey was charged in September on two charges of lying to and obstructing Congress during testimony in late 2020. James was charged in October on two counts of bank fraud and making false statements to a financial institution. Both Comey and James pleaded not guilty to the charges they were facing.

Top Justice Department officials spent Tuesday debating possible courses for their appeal to take.

Some officials entered the day viewing any effort to try to re-indict Comey or save the case as quixotic and bound to fail, given the thorough rejection by the judge.

But Attorney General Pam Bondi’s comments following the ruling Monday — that the Justice Department will take “all available legal action,” including an “immediate appeal” — made clear the department would attempt to find a way to save the Comey charges filed in September, which they continue to view as valid.

Who is driving the bus?

For more than 24 hours, there was a scramble among prosecutors who were left to decide what moves they could make in other criminal cases going forward, according to people familiar with the prosecutors’ office. The Justice Department is still, as of Tuesday afternoon, determining what is next in the cases they have prioritized against James and Comey.

At first, on Monday, some of the prosecutors in the district stopped filing documents in cases all together. It was unclear if Halligan’s name could legally be on them, or who should be listed instead as of the top prosecutors.

Other career prosecutors in the office wondered about the best way forward with grand juries that were set to meet in Alexandria before Thanksgiving — and whether those proceedings could keep moving toward indictments during this time.

The judge’s ruling that invalidated Halligan’s authority said it was the federal court judges in the district who had authority to appoint a new interim US attorney.

About three hours after the ruling Monday, however, the deputy criminal chief in the office told prosecutors to begin listing the first assistant of the office, Robert McBride, who had arrived a week before in that job, as the top prosecutor on case filings.

About an hour later, though, another official in the office emailed all its employees: “The change to the signature block was premature. Please return to the use of Lindsey Halligan, United States Attorney.”

By the close of business Monday, the office’s work was still in flux.

Some filings that had been scheduled before Thanksgiving were pushed to next week.

While some prosecutors were unsure of how to sign their filings, a handful of them on Tuesday filed court documents in active criminal matters in the district’s four Virginia courthouses that listed Halligan as US attorney, as they were directed.

When it comes to the cases against Comey and James, prosecutors feared what might happen if the office tried again — especially given that one of the magistrate judges on the bench this week had recently slammed Halligan in an opinion. That judge, William Fitzpatrick, had read the grand jury transcript in Comey’s case and said Halligan and the FBI had made evidentiary and legal missteps in their interactions with Comey’s grand jurors.

Fitzpatrick is also scheduled to preside in the magistrate court on Wednesday — when the Justice Department may have more clarity to its next steps in the Comey and James cases, and grand jury activity in the courthouse could happen.

The Deputy Attorney General’s Office was still giving little to no legal guidance on the Department’s thinking as of Tuesday afternoon about how to proceed. The thinking divided into a few possible paths forward: Appeal both cases; or attempt to re-indict Comey or James or both.

Assistant US attorneys working on the James case are under less of a perceived charging deadline. Unlike in Comey’s case, where there was a statute of limitations of September to bring the charged against them, James’ prosecutors have a longer runway. On Tuesday, they were in discussion with Justice Department headquarters on what to do next.

But the Comey case — the centerpiece of a trio of indictments the President wanted — came with different issues.

While Judge Cameron Currie wrote in dismissing the case that her decision was “without prejudice,” meaning prosecutors weren’t barred from trying again, she also noted that Halligan’s efforts in the grand jury weren’t valid. The judge said that means there may not have been a valid indictment that prosecutors could now correct — and the five-year window to bring a charge against Comey may have closed at the end of September.

Comey’s defense lawyers maintain they don’t believe a new indictment is possible.

James Pearce, a former federal prosecutor and now senior counsel at the Washington Litigation Group, said the judge’s order Monday suggested Comey could not be re-indicted.

“I think the thrust of the opinion suggested that the judge did not believe he could face re-indictment,” Pearce said, adding that if he were a prosecutor on this case, he would be worried that a judge would side with Comey’s team and decide that the case cannot be indicted again in any district. Pearce was among the lawyers who defended special counsel Jack Smith’s work in the cases against Trump, one of which was similarly dismissed when a judge found Smith didn’t have authority to bring the case.

Patrick Cotter, another former federal prosecutor who now practices at UB Greensfelder, said Currie was not explicit enough when addressing the statute of limitations issue, leaving an interpretation open for Comey to be indicted again quickly on the same charges.

“In her opinion yesterday, she just didn’t address it. She said, ‘I’m just putting you back where you were the day before Halligan showed up,’” Cotter said.

The status of Lindsey Halligan

In the 24 hours after the dismissal of the criminal cases against James Comey and Letitia James, Lindsey Halligan was no where to be found around the office she had led.

Never one to make small talk with career prosecutors during the nine weeks she served as the interim US attorney in the Eastern District of Virginia, Halligan gave no direction Monday or Tuesday on what to do next after a judge invalidated her authority. The Justice Department was saying they stood behind her still.

A Justice Department spokesman said Halligan remains the top prosecutor in the US attorney’s office.

“Yesterday’s order did not remove Lindsey Halligan and as the Attorney General said we intend to appeal,” the spokesman said in a statement Tueday.

Prosecutors in the Eastern District of Virginia, however, found themselves without clarity in their day-to-day duties.

When asked Tuesday if Halligan was still leading the office and how they were operating following the ruling, one prosecutor told CNN, with a shrug, “We’re still working.”

Pearce said that “squishy” was a good term to describe Halligan’s status as the top prosecutor in the office.

“I think under the district court’s ruling, Halligan is not validly serving as the US attorney and not validly presiding over the James and Comey cases, but also not validly serving over, kind of anything that’s going on in the office,” Pearce said. “Though the opinions yesterday didn’t purport to address that question, because it was only specific to those two prosecutions.”

Cotter’s view was the same as Pearce’s, saying that while Bondi may have appointed Halligan as a special attorney, which is typically a designation any assistant US attorney can receive, that is far different from her serving as a US attorney, a political role governed by presidential appointment laws.

“She certainly was not part, legally, of the Department of Justice at the time she obtained these indictments. That’s what the court said,” Cotter said.

What the Alexandria office needs to figure out, and soon

The district court still hasn’t sworn in a new US attorney.

Some around the court believed Tuesday the judges wouldn’t choose a new US attorney, as Currie ruled should happen, because of fear the executive branch would fire that person. And so Halligan may just continue serving, if the Justice Department keeps listing her on briefs, despite the court orders.

And by Tuesday afternoon, the Justice Department still hadn’t notified the judges over the Comey and James cases that they planned to appeal — typically a simple filing that can be prepared quickly.

Pearce stressed that usually, most US attorneys’ offices are filled with career prosecutors that can continue to function normally without a clear leader. However, with the lack of a US attorney, there may not be someone in the office making tough policy decisions.

“I would think there is a fair amount of uncertainty about who’s in charge and who’s making those calls at the moment,” Pearce said.

Cotter also said that for prosecutors in the Eastern District of Virginia office, morale has to be low given all they have endured over the past few months — including the departure of Halligan’s predecessor, Erik Siebert, after facing pressure to bring cases against Comey and James.

“I can’t imagine the turmoil at that office, with Siebert having left the way he did, with Halligan coming in now with this,” Cotter said. “It’s just hard to imagine how there’s much morale left after all this.”

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