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A pair of prominent opponents of President Trump secured major court wins on the start of the week when a US judge dismissed the government's charges filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained fiercely that they are innocent, asserting that the president and justice department are simply targeting them for retaliation.

US District Judge Cameron Currie dismissed the indictments in their cases due to attorney Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the federal authorities to refile the case.

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Comey admitted that possibility after the ruling, stating he believes Trump is likely to target him again.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the government confronts steep hurdles to successfully prosecute both after this setback, and legal analysts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

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

US Attorney General Pam Bondi indicated she would pursue this option, pledging to use all legal means, including an expedited appeal.

Previously, the former administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its petitions up to the US Supreme Court.

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

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

Is it possible there be fresh indictments?

The federal prosecutors charged Comey with making false statements to Congress and obstruction of justice. Federal prosecutors indicted James with bank fraud and making false statements to a bank.

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

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

Based on my analysis, a different attorney could bring James' case to a different grand jury and secure a new indictment, said 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 assigned and is able to secure an indictment.

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

It might be more difficult for the government to try to file the exact same charges against James Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to indict him for these particular claims – which expired at the end of September. However, the indictment's dismissal would trigger a six-month grace period for the DOJ to bring the case again.

Still in that situation, his lawyers said it plans to argue the prosecution is past the deadline.

The ruling also suggests that since the charge is invalid, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

The judge stated in the James decision that the Attorney General's attempt to appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

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

US attorneys are nominated by the US president and need US Senate confirmation. Federal statutes regulate how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's appointment had violated these regulations.

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

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

But Bondi said on Monday that she designated her a special US attorney and praised her work as outstanding.

The White House maintained its position that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.