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Two prominent opponents of former President Trump secured major court wins on Monday when a federal judge threw out the government's charges filed against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, claiming that the administration and DOJ are merely singling out them for retaliation.

Federal Judge Cameron Currie dismissed the charges in their cases due to prosecutor Lindsey Halligan's invalid appointment as US attorney. However, she left the door open for the government to refile the case.

• Judge dismisses cases against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have tainted Comey case
• What is ex-FBI director James Comey accused of?

Comey admitted that likelihood after the ruling, stating he thinks the former president will probably come after him once more.

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

But the government confronts steep hurdles to effectively try both after this defeat, and experts hesitate to predict what could happen 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.

Could the justice department appeal?

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

US Attorney General Pam Bondi indicated she would pursue this option, vowing to use all available legal action, including an immediate appeal.

Previously, the Trump administration has strongly challenged unfavourable rulings, moving cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to continue to challenge any further politically motivated charges through every lawful means available.

In the event of an appeal, the DOJ probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal uncertain.

Is it possible there be fresh indictments?

The government charged Comey with making false statements to lawmakers and obstructing justice. Government lawyers charged James with bank fraud and providing false information to a bank.

Both pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, they also asserted to be targets of vindictive prosecution.

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

Based on my analysis, a new prosecutor could present James's case to a new grand jury and get a new indictment, said Ms Levine.

But legal expert John Day, head 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 Mr Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He described the complex web of attorneys, judges, and motions involved as a procedural morass with no easy solutions.

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

A key issue is the statute of limitations – the time frame that prosecutors had to charge Comey for these particular claims – which expired at the end of September. However, the indictment's dismissal would activate a half-year extension for the DOJ to refile the case.

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

The ruling also suggests that since the indictment is invalid, the time limit has run 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 Comey and James, Judge Currie was direct: Halligan's appointment was improper.

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

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

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

That leaves Halligan's role on future cases against James and Comey, once more, unclear.

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

But Attorney General Bondi said on Monday that she designated Halligan a special US attorney and commended her work as outstanding.

The administration maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.