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A pair of prominent opponents of President Trump obtained major court wins on the start of the week when a US judge dismissed the federal indictments filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are not guilty, asserting that the administration and DOJ are merely singling out them for revenge.

Federal Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. But she also left open the possibility for the federal authorities to try again.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• Federal judge states government 'missteps' may have tainted the Comey trial
• What is ex-FBI director James Comey accused of?

Comey admitted that possibility after the decision, stating he believes the former president is likely to come after him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the final word on this issue.

But the government faces significant obstacles to effectively try both after this defeat, and legal analysts hesitate to forecast what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Kay Levine, law professor at Emory University.

Might the DOJ appeal?

The Department of Justice can challenge Judge Currie's ruling before a federal appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

Attorney General Pam Bondi signaled she would take this route, pledging to use all available legal action, including an immediate appeal.

In other cases, the former administration has aggressively appealed adverse decisions, moving cases from trial courts and sometimes accelerating its petitions up to the Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any additional politically motivated charges through all legal avenues.

If there is an appeal, the DOJ likely would have its own attorneys argue the case, making Halligan's involvement in the appeal uncertain.

Could there be new charges?

The government charged Comey with making false statements to Congress and obstructing justice. Federal prosecutors indicted Letitia James with bank fraud and making false statements to a bank.

Both entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, both also asserted to be victims of vindictive prosecution.

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to convene fresh grand juries and obtain new charges.

As far as everything I've seen, a different attorney could bring James' case to a new grand jury and get a fresh indictment, stated Ms Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

I can tell you it will be hotly contested, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

He described the tangle of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

It could be more difficult for the DOJ to try to file the identical accusations against Comey.

A key issue is the legal time limit – the deadline that prosecutors had to indict Comey for these specific allegations – which ended at the close of September. However, the indictment's dismissal would activate a half-year extension for the justice department to bring the case again.

Still in that situation, his legal team said it intends to contend the prosecution is out of time.

The decision further indicates that since the indictment is void, the time limit has run and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

In both decisions on the charges against James and Comey, the judge was direct: Halligan's appointment was improper.

Judge Currie wrote in the James decision that the Attorney General's attempt to install Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

As a result, she lacked legal power to present the indictment, she wrote.

US attorneys are proposed by the president and require Senate approval. Federal statutes regulate how people can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

That leaves Halligan's position on subsequent cases against James and Comey, again, uncertain.

The decision might also cast a shadow on any other cases Halligan has brought in the Eastern District of Virginia where she serves.

But Bondi said on Monday that she made Halligan a special US attorney and praised her work as excellent.

The administration maintained its position that Halligan's appointment was legal, press secretary Karoline Leavitt told the press on Monday.