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A pair of high-profile opponents of President Trump secured major court wins on Monday when a US judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have maintained fiercely that they are innocent, claiming that the president and justice department are simply singling out them for revenge.

Federal Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's invalid appointment as US attorney. But she also left the door open for the federal authorities to refile the case.

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Comey acknowledged that likelihood after the ruling, stating he thinks Trump is likely to come after him again.

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

But the DOJ confronts significant hurdles to effectively try both after this setback, and legal analysts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, stated Professor Kay Levine, law professor at Emory University.

Might the DOJ challenge the ruling?

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

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

Previously, the former administration has aggressively appealed adverse decisions, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically driven indictments through all legal avenues.

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

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to Congress and obstructing justice. Federal prosecutors indicted Letitia James with bank fraud and making false statements to a financial institution.

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

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

As far as everything I've seen, 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 complex process – certainly in the Comey matter.

It's clear that it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

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

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

One problem is the statute of limitations – the time frame that prosecutors had to charge Comey for these particular claims – which ended at the end of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the justice department to bring the case again.

Even so in that case, his lawyers said it plans to contend the prosecution is past the deadline.

The ruling also suggests that because the charge is void, the time limit has expired and there can be no further indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of prosecutor Lindsey Halligan?

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

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

Therefore, Halligan had no lawful authority to present the indictment, she wrote.

US attorneys are nominated by the US president and need US Senate confirmation. US laws govern how individuals can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these laws.

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

The decision might also cast a shadow on other cases Halligan has brought 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, spokesperson Karoline Leavitt told the press on Monday.