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

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are not guilty, asserting that the administration and DOJ are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the indictments against them due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. However, she left the door open for the federal authorities to try again.

• Court throws out charges against ex-FBI director Comey and NY attorney general James
• US judge says DOJ errors may have tainted Comey case
• What are ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the decision, stating he thinks the former president is likely to target him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the last chapter on this issue.

But the government faces steep obstacles to effectively try both after this setback, and experts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

The DOJ can contest 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 aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, James's lawyer, vowed to keep fighting any additional politically motivated charges through every lawful means available.

If there is an appeals process, the DOJ likely would have its own attorneys present the arguments, making Halligan's involvement in the appeals process uncertain.

Is it possible there be new charges?

The government accused James Comey with making false statements to lawmakers and obstruction of justice. Federal prosecutors indicted James with bank fraud and providing false information to a bank.

Each pleaded not guilty. In addition to claiming Halligan's appointment was invalid, they also asserted to be targets of retaliatory legal action.

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

As far as everything I've seen, a new prosecutor could bring James' case to a new grand jury and get a new 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.

I can tell you it will be strongly disputed, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an charge.

He characterized the tangle of lawyers, courts, and legal filings involved as a procedural morass with no simple answers.

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

A key issue is the statute of limitations – the deadline that government lawyers had to indict Comey for these specific allegations – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to refile the case.

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

The ruling also suggests that because the indictment is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, Judge Currie was blunt: Halligan was wrongly appointed.

The judge stated in the James decision that the Attorney General's attempt to appoint Halligan as Interim 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.

US attorneys are proposed by the president and require Senate approval. US laws regulate how people can be appointed on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

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

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

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

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