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A pair of high-profile opponents of President Trump secured significant legal victories on the start of the week when a federal judge dismissed the federal indictments filed against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have argued fiercely that they are not guilty, asserting that the administration and DOJ are merely targeting them for retaliation.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment 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 likelihood after the decision, stating he believes the former president will probably come after him again.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the final word on this matter.

But the government confronts significant obstacles to successfully prosecute either after this setback, 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 Professor Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

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

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

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

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically driven indictments through every lawful means available.

If there is an appeal, the justice department probably would have its own attorneys present the arguments, making Halligan's involvement in the appeals process unclear.

Could there be fresh indictments?

The government charged James Comey with making false statements to lawmakers and obstructing justice. Government lawyers indicted Letitia James with bank fraud and providing false information to a bank.

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

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

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

But legal expert 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 lawfully appointed prosecutor is appointed and is can obtain an charge.

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

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

One problem is the legal time limit – the deadline that government lawyers had to indict him for these particular claims – which expired at the end of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the DOJ to bring the case again.

Still in that situation, his legal team said it plans to argue the government is out of time.

The ruling also suggests that because the indictment is invalid, the time limit has expired and there can be no new 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 was wrongly appointed.

Judge Currie wrote in the James decision that the AG's effort to install Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

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

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

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

The decision might also cast a shadow on any 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 US attorney and commended her work as excellent.

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