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A pair of prominent critics of President Trump achieved major court wins on Monday when a federal judge dismissed 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 fiercely that they are not guilty, claiming that the president and justice department are simply targeting them for revenge.

US District Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's invalid assignment as US attorney. However, she left the door open for the federal authorities to refile the case.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that likelihood after the ruling, stating he thinks the former president will probably target him once more.

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

But the government faces 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.

Could the justice department challenge the ruling?

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

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

In other cases, the former administration has strongly challenged adverse decisions, taking cases from lower courts and sometimes fast-tracking 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 DOJ likely would have its own attorneys argue the case, making Halligan's involvement in the appeal unclear.

Could there be new charges?

The federal prosecutors charged Comey with lying to Congress and obstructing justice. Government lawyers indicted James with bank fraud and providing false information to a bank.

Both pleaded not guilty. In addition to claiming Halligan's appointment was invalid, they also claimed to be targets of vindictive prosecution.

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

As far as everything I've seen, a new prosecutor could present James's case to a different grand jury and get a fresh indictment, stated Ms Levine.

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

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

He characterized the tangle of attorneys, judges, 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 Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to indict him for these particular claims – which expired at the end 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 lawyers said it plans to contend the prosecution is out of time.

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

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the charges against James and Comey, Judge Currie was direct: Halligan's appointment was improper.

The judge stated in the James decision that the AG's effort to install Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

As a result, she had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are nominated by the president and require US Senate confirmation. Federal statutes regulate how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these laws.

That leaves Halligan's role on future cases against both individuals, once more, unclear.

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 made Halligan a special federal prosecutor and commended her work as outstanding.

The administration stood by its stance that Halligan's appointment was legal, press secretary Karoline Leavitt told reporters on Monday.