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A pair of well-known critics of President Trump obtained significant court wins on Monday when a US judge threw out the federal indictments filed against them.

For 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 president and justice department are merely targeting them for revenge.

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

• Court throws out cases against ex-FBI director Comey and NY attorney general James
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• What is former FBI head James Comey accused of?

Comey admitted that likelihood after the decision, saying he thinks Trump is likely to come after 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 DOJ faces significant hurdles to effectively try both after this setback, and experts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

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

Might the DOJ challenge the ruling?

The DOJ can challenge Judge Currie's ruling 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 pursue this option, pledging to use all available legal action, including an expedited appeal.

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

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

If there is an appeals process, the justice department probably would have its own attorneys present the arguments, making Halligan's role in the appeal unclear.

Could there be fresh indictments?

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

Each entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, both also claimed to be victims of vindictive prosecution.

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

Based on my analysis, a different attorney could bring James' case to a new grand jury and secure 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 the Comey matter.

It's clear that it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is able to secure an indictment.

He described the complex web of lawyers, judges, and motions involved as a procedural morass with no easy solutions.

It might be harder for the government to try to bring the identical accusations against Comey.

One problem is the legal time limit – the time frame that prosecutors had to indict Comey for these specific allegations – which ended at the close of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to bring the case again.

Even so in that situation, his legal team said it plans to argue the prosecution is past the deadline.

The decision further indicates that because the charge is void, the time limit has expired and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

In both decisions on the indictments against James and Comey, Judge Currie was blunt: Halligan's appointment was improper.

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

Therefore, she lacked legal power to file the charges, the judge wrote.

Federal prosecutors are nominated by the US president and require Senate approval. US laws regulate how individuals can be appointed on a temporary basis, but the judge determined that Halligan's assignment had violated these regulations.

That leaves Halligan's position on subsequent cases against James and Comey, again, unclear.

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

But Bondi said on that day that she designated Halligan a special federal prosecutor and praised her work as outstanding.

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