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A pair of high-profile critics of President Trump secured significant legal victories on Monday when a federal judge threw out the government's charges filed against them.

Over recent weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have insisted fiercely that they are innocent, asserting that the administration and DOJ 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 federal prosecutor. But she also left the door open for the government to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
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• What is ex-FBI director James Comey accused of?

Comey acknowledged that likelihood after the decision, saying he believes the former president is likely to come after him once more.

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

But the government confronts significant obstacles 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, stated Kay Levine, law professor at Emory University.

Might the DOJ appeal?

The DOJ can challenge Judge Currie's ruling before a federal appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

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

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

Attorney Abbe Lowell, James's lawyer, pledged to keep fighting any additional politically motivated charges through all legal avenues.

If there is an appeal, the DOJ likely would have its own attorneys argue the case, making Halligan's involvement in the appeals process unclear.

Is it possible there be new charges?

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

Each pleaded not guilty. Besides arguing Halligan was unlawfully appointed, they also claimed to be victims of retaliatory legal action.

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

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

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly 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 assigned and is able to secure an charge.

He described the complex web of attorneys, courts, and motions involved as a procedural morass with no simple answers.

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

A key issue is the statute of limitations – 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 half-year extension for the DOJ to refile the case.

Even so in that case, his legal team said it plans to contend the government is out of time.

The decision further indicates that since the charge is void, the time limit has expired and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

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

Therefore, she lacked legal power to present the indictment, she wrote.

US attorneys are proposed by the president and need US Senate confirmation. Federal statutes regulate how people can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had breached these laws.

This makes Halligan's position on future cases against both individuals, again, uncertain.

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

But Bondi said on that day that she made her a special federal prosecutor and praised her work as outstanding.

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.