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A pair of high-profile critics of former President Trump achieved major court wins on Monday when a federal judge dismissed the federal indictments filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have argued fiercely that they are not guilty, claiming that the president and justice department are merely singling out them for revenge.

US District Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. But she also left open the possibility for the federal authorities to refile the case.

• Judge dismisses cases against former FBI chief Comey and NY attorney general James
• Federal judge states government 'missteps' may have tainted Comey case
• What are ex-FBI director James Comey charged with?

Comey admitted that possibility after the ruling, stating 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 last chapter on this matter.

But the government faces significant obstacles to successfully prosecute either after this setback, and experts hesitate to forecast what could happen next due to the unprecedented circumstances of the cases.

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

Could the justice department appeal?

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

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

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

Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically motivated charges through every lawful means available.

In the event of an appeals process, the justice department likely would have its own lawyers argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstructing justice. Government lawyers indicted Letitia James with financial fraud and providing false information to a financial institution.

Each pleaded not guilty. In addition to arguing Halligan's appointment was invalid, they also claimed to be victims of vindictive prosecution.

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

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and get a new indictment, stated Professor Levine.

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – especially in Comey's case.

It's clear that it will be strongly disputed, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an indictment.

He characterized the tangle of lawyers, judges, and motions involved as a procedural morass with no easy solutions.

It might be more difficult for the government to try to bring the identical accusations against Comey.

One problem is the legal time limit – the deadline that prosecutors had to indict Comey for these specific allegations – which ended at the close of September. Nonetheless, the indictment's dismissal would activate a half-year extension for the justice department to bring the case again.

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

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

What happens to Lindsey Halligan?

In both decisions on the indictments against James and Comey, the judge was blunt: Halligan's appointment was improper.

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.

As a result, Halligan lacked legal power to file the charges, she wrote.

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

That leaves Halligan's role on subsequent cases against both individuals, once more, uncertain.

The decision might also cast a shadow on other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

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

The White House stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.