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A pair of high-profile critics of President Trump achieved significant court wins on the start of the week when a US judge threw out the federal indictments filed against them.

For weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have maintained fiercely that they are innocent, claiming that the president and justice department are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid appointment as US attorney. However, she left open the possibility for the federal authorities to refile the case.

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

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

But the DOJ confronts significant hurdles 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 uncharted territory, stated Professor Kay Levine, Emory University School of Law professor.

Might the justice department appeal?

The Department of Justice can contest the judge's decision 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, pledging to use all available legal action, including an immediate appeal.

In other cases, the former administration has aggressively appealed unfavourable rulings, moving cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

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

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

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to Congress and obstructing justice. Federal prosecutors charged Letitia James with financial fraud and making false statements to a bank.

Each entered not guilty pleas. Besides arguing Halligan's appointment was invalid, they also asserted to be victims of retaliatory legal action.

Since the initial charges were dismissed (though, of course, appeals could change that), the government might try to convene fresh grand juries and secure new indictments.

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

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – certainly in the Comey matter.

It's clear that it will be strongly disputed, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an charge.

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

It could be harder for the government to try to file the exact same charges against James Comey.

One problem is the statute of limitations – the time frame that government lawyers had to indict Comey for these specific allegations – which expired at the close of September. However, the dismissal of the charges would activate a half-year extension for the justice department to bring the case again.

Still in that situation, his lawyers said it intends to argue the government is past the deadline.

The decision further indicates that since the charge is invalid, the time limit has run and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, the judge was blunt: Halligan was wrongly appointed.

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

As a result, Halligan lacked legal power to present the indictment, the judge wrote.

Federal prosecutors are proposed by the US president and require US Senate confirmation. US laws govern how individuals can be assigned on a temporary basis, but the judge determined that Halligan's appointment had violated these laws.

That leaves Halligan's role on subsequent cases against James and Comey, again, uncertain.

The ruling also could cast a shadow on any other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

But Bondi said on that day that she made her a special US attorney and praised her work as outstanding.

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.