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Two prominent critics of President Trump achieved significant legal victories on Monday when a federal judge threw out the federal indictments filed against them.

For weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, asserting that the administration and DOJ are merely targeting them for revenge.

Federal Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. But she also left open the possibility for the federal authorities to refile the case.

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Comey acknowledged that possibility after the decision, saying he thinks the former president is likely to come after him again.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the DOJ confronts significant hurdles to successfully prosecute both after this setback, and experts hesitate 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 Department of Justice can challenge Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

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

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

If there is an appeals process, the DOJ likely would have its own lawyers present the arguments, making Halligan's role in the appeals process unclear.

Could there be new charges?

The federal prosecutors charged Comey with making false statements to Congress and obstruction of justice. Federal prosecutors indicted Letitia James with bank fraud and providing false information to a bank.

Each pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, both also claimed to be victims of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to convene fresh 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 get a new indictment, stated Ms Levine.

But legal expert John Day, president 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 Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He characterized the complex web of lawyers, courts, and legal filings involved as a legal quagmire with no simple answers.

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

A key issue is the statute of limitations – the deadline 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 half-year extension for the DOJ to refile the case.

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

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

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, the judge was blunt: Halligan's appointment was improper.

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

As a result, she had no lawful authority to present the indictment, the judge wrote.

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

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

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

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

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