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Two prominent opponents of President Trump obtained significant court wins on the start of the week when a federal 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 vehemently that they are not guilty, claiming that the president and justice department are merely singling out them for retaliation.

US District Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. But she also left open the possibility for the federal authorities to refile the case.

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Comey admitted that possibility after the decision, saying he thinks the former president is likely to come after him again.

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

But the DOJ faces significant obstacles to effectively try both after this defeat, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Professor Kay Levine, law professor at Emory University.

Might the justice department challenge the ruling?

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

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

In other cases, the Trump administration has strongly challenged adverse decisions, moving cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any additional politically driven indictments through all legal avenues.

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

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstructing justice. Government lawyers indicted James with financial fraud and making false statements to a bank.

Both entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, they also asserted to be targets of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the government might try to assemble fresh 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 get a new indictment, stated Professor Levine.

But John Day, head of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an charge.

He characterized the complex web of attorneys, courts, and legal filings involved as a procedural morass with no easy solutions.

It might be harder for the DOJ to try to file the identical accusations against James Comey.

One problem is the statute of limitations – the deadline that prosecutors had to charge Comey for these specific allegations – which ended at the end of September. However, the dismissal of the charges would activate a half-year extension for the DOJ to refile the case.

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

The decision further indicates that since the charge is void, the statute of limitations has expired and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the charges against James and Comey, Judge Currie was blunt: Halligan was wrongly appointed.

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

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

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

That leaves Halligan's position on future cases against both individuals, again, uncertain.

The ruling also could raise doubts on any other cases Halligan has brought in the Virginia Eastern District where she serves.

But Attorney General Bondi said on Monday that she designated Halligan a special federal prosecutor and praised her work as excellent.

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