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A pair of high-profile opponents of former President Trump obtained major court wins on the start of the week when a federal judge threw out the federal indictments against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. But she also left open the possibility for the government to refile the case.

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Comey acknowledged that likelihood after the decision, saying he believes the former president will probably target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the final word on this issue.

But the government faces significant obstacles to successfully prosecute both after this setback, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

The DOJ can contest the judge's decision before a federal appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

Previously, the Trump administration has strongly challenged unfavourable rulings, moving cases from lower courts and sometimes fast-tracking its petitions up to the Supreme Court.

Abbe Lowell, James's lawyer, vowed 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 involvement in the appeals process uncertain.

Could there be fresh indictments?

The government accused James Comey with making false statements to Congress and obstruction of justice. Federal prosecutors charged Letitia James with financial fraud and providing false information to a financial institution.

Both entered not guilty pleas. In addition to claiming Halligan was unlawfully appointed, they also claimed to be targets of retaliatory legal action.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to assemble fresh grand juries and secure new charges.

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

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in Comey's case.

It's clear that it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

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

It could be more difficult for the DOJ to try to file the identical accusations against Comey.

One problem is the statute of limitations – the deadline that prosecutors had to charge Comey for these specific allegations – which expired at the end of September. However, the indictment's dismissal would trigger a six-month grace period for the justice department to bring the case again.

Still in that situation, his legal team said it intends to argue the prosecution is past the deadline.

The decision further indicates that because the indictment is invalid, the time limit has expired and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against James and Comey, the judge was direct: Halligan was wrongly appointed.

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

Therefore, Halligan had no lawful authority to file the charges, she wrote.

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

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

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

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

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