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Two prominent opponents of former President Trump obtained significant court wins on Monday when a US judge threw out the government's charges filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are innocent, claiming that the president and justice department are merely singling out them for revenge.

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

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Comey acknowledged that possibility after the decision, stating he believes Trump is likely to come after him again.

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

But the government confronts steep obstacles to effectively try both after this setback, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

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

Could the justice department challenge the ruling?

The DOJ can challenge Judge Currie's ruling before a federal appeals court. In this case, that would be the Fourth Circuit Appeals Court.

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

In other cases, the Trump administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically driven indictments through all legal avenues.

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

Could there be fresh indictments?

The federal prosecutors charged James Comey with lying to Congress and obstruction of justice. Government lawyers indicted James with bank fraud and providing false information to a financial institution.

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

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to assemble fresh grand juries and secure new indictments.

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

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

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 charge.

He characterized the complex web of attorneys, courts, and legal filings involved as a procedural morass with no simple answers.

It might be harder for the DOJ to try to file the identical accusations against Comey.

One problem is the statute of limitations – the time frame that prosecutors had to indict him for these particular claims – which expired at the close of September. However, the indictment's dismissal would activate a half-year extension for the justice department to bring the case again.

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

The ruling also suggests that because the indictment is void, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, Judge Currie was direct: Halligan was wrongly appointed.

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

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

US attorneys are nominated by the US president and need Senate approval. Federal statutes govern how people can be appointed on a interim basis, but Judge Currie found that Halligan's appointment had violated these laws.

This makes Halligan's position on subsequent cases against James and Comey, again, uncertain.

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

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

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