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Two high-profile critics of former President Trump secured significant court wins on Monday when a US judge threw out the government's charges against them.

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

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

• Judge dismisses charges against former FBI chief Comey and New York AG James
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• What is ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the decision, stating he thinks Trump will probably target him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this issue.

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

It feels to me like unexplored legal ground, 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.

US Attorney General Pam Bondi signaled she would take this route, pledging to use all legal means, including an expedited appeal.

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

Abbe Lowell, James's lawyer, pledged to keep fighting any further politically driven indictments through all legal avenues.

If there is an appeal, the DOJ likely would have its own lawyers present the arguments, making Halligan's involvement in the appeal uncertain.

Is it possible there be fresh indictments?

The government charged Comey with lying to lawmakers and obstructing justice. Federal prosecutors charged James with financial fraud and making false statements to a financial institution.

Each pleaded not guilty. Besides claiming Halligan was unlawfully appointed, both also claimed to be victims of retaliatory legal action.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to assemble new grand juries and secure new charges.

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

But John Day, head of the American College of Trial Lawyers, said it could be a complicated path – especially 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 assigned and is able to secure an charge.

He described the tangle of lawyers, courts, and legal filings involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to file the exact same charges against Comey.

One problem is the statute of limitations – the time frame that prosecutors had to charge Comey for these specific allegations – which expired at the close of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department to refile the case.

Still in that case, his legal team said it intends to argue 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, lawyer Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, the judge was blunt: Halligan's appointment was improper.

The judge stated in the James ruling that the Attorney General's attempt to appoint Halligan as Acting US Attorney for the Virginia Eastern District was unlawful.

Therefore, she had no lawful authority to present the indictment, she wrote.

US attorneys are proposed by the US president and require Senate approval. US laws govern how individuals can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had breached these laws.

This makes Halligan's role on future cases against James and Comey, once more, uncertain.

The ruling also could cast a shadow on any other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

But Bondi said on that day that she designated Halligan a special US attorney and commended her work as excellent.

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