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

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

US District Judge Cameron Currie tossed the indictments in their cases due to attorney Lindsey Halligan's invalid appointment as US attorney. But she also left the door open for the government to refile the case.

• Court throws out cases against ex-FBI director Comey and NY attorney general James
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Comey admitted that likelihood after the ruling, saying he thinks the former president will probably come after him once more.

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

But the government confronts steep hurdles to effectively try both after this defeat, and legal analysts hesitate to forecast what could happen next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Professor Kay Levine, Emory University School of Law professor.

Could the DOJ challenge the ruling?

The Department of Justice can contest the judge's decision before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

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

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

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

In the event of an appeals process, the justice department probably would have its own lawyers argue the case, making Halligan's involvement in the appeals process uncertain.

Is it possible there be new charges?

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

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

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

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

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

I can tell you it will be strongly disputed, whether Comey's case can be re-indicted if a properly assigned attorney is assigned and is can obtain an indictment.

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

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

One problem is the legal time limit – the time frame that government lawyers had to indict Comey for these particular claims – which expired at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department to bring the case again.

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

The ruling also suggests that since the charge is invalid, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of prosecutor Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

The judge stated in the James ruling that the AG's effort to appoint Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

As a result, Halligan had no lawful authority to file the charges, the judge wrote.

US attorneys are proposed by the US president and need Senate approval. Federal statutes govern how people can be assigned on a temporary basis, but the judge determined that Halligan's assignment had breached these regulations.

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

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

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

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.