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Two well-known opponents of former President Trump obtained major court wins on Monday when a federal judge threw out the federal indictments against them.

For weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have argued fiercely that they are innocent, asserting that the administration and DOJ are simply singling out them for retaliation.

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

• Court throws out cases against former FBI chief Comey and NY attorney general James
• Federal judge states DOJ errors may have compromised Comey case
• What is former FBI head James Comey accused of?

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

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

But the DOJ confronts steep hurdles to effectively try either after this defeat, and legal analysts hesitate to predict what could occur next due to the cases' unprecedented nature.

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

Could the justice department challenge the ruling?

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

Attorney General Pam Bondi signaled she would pursue this option, pledging to use all available legal action, including an expedited appeal.

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

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically motivated charges through all legal avenues.

In the event of an appeal, the justice department likely would have its own attorneys argue the case, making Halligan's involvement in the appeals process uncertain.

Could there be fresh indictments?

The federal prosecutors charged Comey with lying to Congress and obstructing justice. Federal prosecutors charged James with financial fraud and making false statements to a financial institution.

Each pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, both also asserted to be victims of retaliatory legal action.

With the original indictments thrown out (though, of course, appeals could change that), the government might try to assemble new grand juries and secure new indictments.

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and secure a fresh indictment, said Ms 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.

I can tell you it will be strongly disputed, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

He described the tangle of lawyers, courts, and legal filings involved as a legal quagmire with no simple answers.

It could be harder for the government to try to file the exact same charges against James Comey.

A key issue is the legal time limit – the time frame that government lawyers had to charge him for these particular claims – which ended at the close of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to bring the case again.

Even so in that case, his legal team said it plans to argue the prosecution is past the deadline.

The decision further indicates that since the charge is invalid, the statute of limitations has run and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In both decisions on the indictments against Comey and James, the judge was direct: Halligan was wrongly appointed.

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 unlawful.

Therefore, she lacked legal power to present the indictment, the judge wrote.

US attorneys are proposed by the US president and require Senate approval. US laws govern how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these regulations.

That leaves Halligan's position on future cases against both individuals, again, unclear.

The ruling also could cast a shadow on 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 US attorney and praised her work as excellent.

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.