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Two well-known critics of President Trump achieved significant court wins on Monday when a federal judge dismissed the federal indictments filed against them.

Over recent weeks following their charges, former FBI Director 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 singling out them for revenge.

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

• Judge dismisses charges against former FBI chief Comey and New York AG James
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• What is ex-FBI director James Comey accused of?

Comey admitted that possibility after the decision, saying he thinks Trump is likely to target him again.

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

But the DOJ confronts significant hurdles to effectively try both after this setback, and experts hesitate to predict what could happen 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.

Could the justice department challenge the ruling?

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

US Attorney General Pam Bondi indicated she would take this route, vowing to use all available legal action, including an expedited appeal.

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

Abbe Lowell, James's lawyer, vowed to keep fighting any further politically driven indictments through all legal avenues.

If there is an appeal, the justice department likely would have its own attorneys argue the case, making Halligan's involvement in the appeal unclear.

Could there be fresh indictments?

The federal prosecutors accused James Comey with making false statements to Congress and obstructing justice. Government lawyers indicted James with financial fraud and providing false information to a bank.

Both entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, both also claimed to be victims of retaliatory legal action.

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

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and secure a new indictment, said Professor Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – 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 appointed and is can obtain an indictment.

He characterized the tangle of lawyers, courts, and legal filings 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 James Comey.

One problem is the statute of limitations – the deadline that prosecutors had to charge him for these particular claims – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the justice department to refile the case.

Even so in that situation, his lawyers said it plans to argue the prosecution is out of time.

The decision further indicates 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 is the fate of 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 Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

As a result, Halligan had no lawful authority to file the charges, she wrote.

Federal prosecutors are nominated by the president and require US Senate confirmation. Federal statutes regulate how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's assignment had violated these regulations.

That leaves Halligan's role on future cases against both individuals, once more, uncertain.

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 made Halligan a special US attorney and commended her work as excellent.

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