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A pair of well-known opponents of President Trump achieved significant court wins on Monday when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted vehemently that they are innocent, asserting that the administration and DOJ are merely targeting them for retaliation.

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

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Comey admitted that likelihood after the decision, stating he believes the former president is likely to target him again.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the final word on this matter.

But the government confronts significant obstacles to successfully prosecute either after this setback, and legal analysts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, stated Kay Levine, law professor at Emory University.

Might the justice department challenge the ruling?

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

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

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

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

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

Is it possible there be new charges?

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.

Each pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, both also claimed to be targets of retaliatory legal action.

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

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

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

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an charge.

He described the tangle of lawyers, judges, and motions involved as a legal quagmire with no easy solutions.

It could be harder for the DOJ to try to bring the identical accusations against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to charge Comey for these particular claims – which ended at the close of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the DOJ to refile the case.

Even so 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 void, the time limit has run and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

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

The judge stated in the James ruling that the Attorney General's attempt to appoint Ms. Halligan as Interim US Attorney for the Eastern District of Virginia was invalid.

As a result, she lacked legal power to present the indictment, she wrote.

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

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

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

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

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