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A pair of well-known opponents of former President Trump obtained significant court wins on Monday when a federal judge threw out the government's charges filed against them.

Over recent weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, claiming that the president and justice department are simply targeting them for retaliation.

US District Judge Cameron Currie tossed the indictments 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.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that likelihood after the decision, saying he thinks the former president is likely to target him once more.

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

But the government confronts steep hurdles to effectively try both after this setback, 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, said Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

The DOJ can contest the judge's decision 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 take this route, vowing to use all legal means, including an immediate appeal.

Previously, the former administration has strongly challenged unfavourable rulings, moving cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Abbe Lowell, James's lawyer, vowed 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 argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be fresh indictments?

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

Each entered not guilty pleas. Besides arguing Halligan's appointment was invalid, they also asserted to be victims of vindictive prosecution.

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

Based on my analysis, a new prosecutor could bring James' case to a new 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 complicated path – certainly in Comey's case.

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

He described the complex web of lawyers, courts, and motions involved as a procedural morass with no simple answers.

It could be harder for the DOJ to try to bring the exact same charges against Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to indict Comey for these specific allegations – which ended at the close of September. However, the dismissal of the charges would activate a six-month grace period for the justice department to bring the case again.

Even so in that case, his lawyers said it intends 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 Monday.

What is the fate of Lindsey Halligan?

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

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

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

Federal prosecutors are nominated by the US president and require Senate approval. US laws govern how people can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had breached these laws.

This makes Halligan's role on future cases against both individuals, again, uncertain.

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

But Attorney General Bondi said on that day that she made her a special US attorney and praised her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.