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Two high-profile critics of President Trump secured major court wins on Monday when a US judge threw out the federal indictments against them.

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

US District Judge Cameron Currie dismissed the indictments against them due to attorney Lindsey Halligan's improper assignment as federal prosecutor. But she also left open the possibility for the government to refile the case.

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

Comey acknowledged that possibility after the decision, saying he believes Trump is likely to come after him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this issue.

But the DOJ faces steep obstacles to effectively try either after this defeat, and legal analysts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Could the DOJ 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 Court of Appeals.

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 adverse decisions, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically driven indictments through every lawful means available.

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

Is it possible there be new charges?

The federal prosecutors charged Comey with lying to lawmakers and obstructing justice. Government lawyers charged James with financial fraud and making false statements to a financial institution.

Both entered not guilty pleas. Besides claiming Halligan's appointment was invalid, they also asserted to be targets of retaliatory legal action.

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

As far as everything I've seen, a different attorney could bring James' case to a new grand jury and secure a fresh indictment, stated Professor Levine.

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

I can tell you it will be hotly contested, whether Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an charge.

He characterized the tangle of lawyers, courts, and motions involved as a legal quagmire with no easy solutions.

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

One problem is the legal time limit – the deadline that prosecutors had to indict Comey for these particular claims – which ended at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the DOJ to bring the case again.

Even so in that situation, his legal team said it intends to contend the government is out of time.

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

What happens to prosecutor Lindsey Halligan?

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

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

Therefore, she lacked legal power to present the indictment, she wrote.

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

That leaves Halligan's position on future cases against James and Comey, again, uncertain.

The ruling also could raise doubts on other cases Halligan has brought in the Eastern District of Virginia where she works.

But Bondi said on Monday that she made Halligan a special federal prosecutor and commended her work as excellent.

The administration stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.