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A pair of high-profile critics of former President Trump secured significant legal victories on Monday when a federal judge threw out the federal indictments filed against them.

For weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, claiming that the president and justice department are merely targeting them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's invalid appointment as federal prosecutor. However, she left open the possibility for the government to refile the case.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
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Comey acknowledged that likelihood after the ruling, stating he believes the former president will probably come after him again.

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

But the DOJ confronts significant hurdles to effectively try both after this defeat, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

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

Might 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 indicated she would pursue this option, vowing to use all available legal action, including an expedited appeal.

Previously, the Trump administration has aggressively appealed unfavourable rulings, taking cases from trial courts and sometimes fast-tracking its requests up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically driven indictments through every lawful means available.

In the event of an appeals process, the DOJ probably would have its own attorneys present the arguments, making Halligan's role in the appeals process unclear.

Is it possible there be new charges?

The government charged Comey with lying to Congress and obstruction of justice. Government lawyers charged James with bank fraud and making false statements to a bank.

Both entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, they also claimed to be victims of retaliatory legal action.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to convene new grand juries and obtain new indictments.

As far as everything I've seen, a new prosecutor could present James's case to a different grand jury and get a new indictment, said Professor Levine.

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

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

He described the complex web of attorneys, courts, and motions involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to bring the exact same charges against James 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 DOJ to refile the case.

Still in that situation, his lawyers said it intends to argue the government is out of time.

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

What happens to prosecutor Lindsey Halligan?

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

Judge Currie wrote in the James ruling that the AG's effort to install Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

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

Federal prosecutors are nominated by the president and require Senate approval. Federal statutes regulate how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these laws.

This makes Halligan's position on subsequent cases against both individuals, once more, uncertain.

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

But Bondi said on Monday that she designated her a special federal prosecutor and commended her work as outstanding.

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