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A pair of prominent critics of former President Trump achieved major legal victories on the start of the week when a federal judge threw out the federal indictments against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, asserting that the administration and DOJ are merely singling out them for revenge.

US District Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's improper appointment as federal prosecutor. But she also left open the possibility for the federal authorities to try again.

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

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

But the government faces significant obstacles to effectively try either after this defeat, and experts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, stated Kay Levine, Emory University School of Law professor.

Could the DOJ challenge the ruling?

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

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

In other cases, the former administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes accelerating its petitions up to the Supreme Court.

Abbe Lowell, James's lawyer, vowed to continue to challenge any additional politically driven indictments through all legal avenues.

In the event of an appeals process, the DOJ probably would have its own lawyers argue the case, making Halligan's role in the appeal unclear.

Could there be fresh indictments?

The government accused James Comey with lying to lawmakers and obstructing justice. Government lawyers indicted Letitia James with bank fraud and providing false information to a financial institution.

Both pleaded not guilty. Besides claiming Halligan was unlawfully appointed, both also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to assemble new grand juries and secure new indictments.

Based on my analysis, a different attorney could bring James' case to a different grand jury and get a fresh indictment, said Professor Levine.

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

I can tell you it will be strongly disputed, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an charge.

He characterized the complex web of lawyers, judges, and legal filings involved as a legal quagmire with no easy solutions.

It could be harder for the DOJ to try to bring the identical accusations against James Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to indict Comey for these particular claims – which expired at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department to bring the case again.

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

The ruling also suggests that since the indictment is invalid, the statute of limitations has expired and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

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

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

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

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

That leaves Halligan's position on subsequent cases against both individuals, once more, unclear.

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

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

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