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Two well-known opponents of former President Trump achieved major legal victories on the start of the week when a US 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 maintained vehemently that they are innocent, asserting that the president and justice department are merely targeting them for retaliation.

US District Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. But she also left the door open for the government to refile the case.

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Comey acknowledged that possibility after the decision, stating he thinks Trump is likely to target him once more.

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

But the government faces significant hurdles to successfully prosecute either after this setback, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

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

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

Previously, the former administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

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

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

Is it possible there be fresh indictments?

The government charged James Comey with lying to lawmakers and obstruction of justice. Federal prosecutors indicted James with financial fraud and providing false information to a financial institution.

Each entered not guilty pleas. Besides claiming Halligan was unlawfully appointed, they also asserted to be victims of vindictive prosecution.

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

Based on my analysis, a new prosecutor could present James's case to a new 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 complicated path – especially in Comey's case.

It's clear that 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 described the complex web of lawyers, judges, and motions involved as a procedural morass with no easy solutions.

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

One problem is the legal time limit – the time frame that prosecutors had to indict Comey for these specific allegations – which expired at the close of September. However, the dismissal of the charges would trigger a six-month grace period for the DOJ to refile the case.

Still in that situation, his legal team said it intends to contend the prosecution is out of time.

The decision further indicates that because the charge is invalid, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In the pair of rulings on the charges against James and Comey, the judge was direct: 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 unlawful.

Therefore, she lacked legal power to file the charges, the judge wrote.

Federal prosecutors are nominated by the US president and need Senate approval. US laws govern how individuals can be assigned on a interim basis, but Judge Currie found that Halligan's appointment had breached these regulations.

This makes Halligan's role on subsequent cases against both individuals, again, uncertain.

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

But Attorney General Bondi said on that day that she designated Halligan a special US attorney and praised her work as outstanding.

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.