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A pair of prominent critics of President Trump achieved major court wins on Monday when a US judge threw out the government's charges filed against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have maintained fiercely that they are innocent, claiming that the president and justice department are simply singling out them for revenge.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's invalid assignment as US attorney. But she also left the door open for the government to refile the case.

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Comey acknowledged that likelihood after the ruling, stating he thinks the former president is likely to come after him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the last chapter on this issue.

But the government confronts steep obstacles to successfully prosecute both after this defeat, and legal analysts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

The DOJ can contest 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 indicated she would take this route, vowing to use all legal means, including an immediate appeal.

Previously, the Trump administration has strongly challenged unfavourable rulings, moving cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeals process, the DOJ probably would have its own lawyers argue the case, making Halligan's involvement in the appeal uncertain.

Could there be fresh indictments?

The government charged James Comey with lying to Congress and obstructing justice. Federal prosecutors charged James with financial fraud and providing false information to a financial institution.

Each pleaded not guilty. In addition to arguing Halligan's appointment was invalid, both also claimed to be victims of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to assemble fresh grand juries and obtain new indictments.

Based on my analysis, a new prosecutor could present James's case to a new grand jury and get a fresh indictment, said Ms Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – especially in the Comey matter.

I can tell you it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an charge.

He characterized the tangle of attorneys, courts, and legal filings involved as a procedural morass with no simple answers.

It might be more difficult for the DOJ to try to bring the identical accusations against Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to indict Comey for these particular claims – which ended at the close of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the DOJ to refile the case.

Still in that situation, his lawyers said it intends to contend the government is past the deadline.

The ruling also suggests that since the charge is void, the time limit has expired and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In the pair of rulings on the charges against James and Comey, Judge Currie was direct: Halligan was wrongly appointed.

Judge Currie wrote in the James decision that the AG's effort to appoint Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

Federal prosecutors are nominated by the president and require US Senate confirmation. US laws govern how individuals can be assigned on a interim basis, but the judge determined that Halligan's appointment had breached these regulations.

That leaves Halligan's role on subsequent cases against both individuals, once more, uncertain.

The decision might also raise doubts on any other cases Halligan has brought in the Virginia Eastern District where she serves.

But Bondi said on that day that she made her a special federal prosecutor and praised her work as excellent.

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