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A pair of well-known opponents of former President Trump secured significant legal victories on Monday when a federal judge threw out the federal indictments against them.

For weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have insisted vehemently that they are not guilty, claiming that the president and justice department are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. However, she left open the possibility for the federal authorities to try again.

• Court throws out cases against ex-FBI director Comey and New York AG James
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• What are former FBI head James Comey accused of?

Comey admitted that likelihood after the ruling, saying he believes the former president is likely to target him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this matter.

But the government faces steep obstacles to effectively try either after this setback, and experts hesitate to predict what could occur next due to the cases' unprecedented nature.

In my view, it's uncharted territory, said Kay Levine, Emory University School of Law professor.

Might the justice department appeal?

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.

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

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

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically driven indictments through every lawful means available.

In the event of an appeal, the DOJ likely would have its own attorneys argue the case, making Halligan's role in the appeal unclear.

Is it possible there be fresh indictments?

The government accused Comey with making false statements to Congress and obstruction of justice. Federal prosecutors 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, both 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 assemble fresh grand juries and obtain new charges.

Based on my analysis, a new prosecutor could bring James' case to a different grand jury and get a fresh indictment, said Professor 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 hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an indictment.

He described the tangle of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

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

A key issue is the legal time limit – the time frame that prosecutors had to charge him for these particular claims – which ended at the close of September. However, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

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

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

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, the judge was direct: Halligan was wrongly appointed.

The judge stated in the James ruling that the AG's effort to appoint Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

Therefore, she had no lawful authority to file the charges, she wrote.

Federal prosecutors are nominated by the president and require US Senate confirmation. US laws govern how individuals can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these laws.

This makes Halligan's position on future cases against both individuals, once more, uncertain.

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

But Bondi said on Monday that she made her 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 reporters on Monday.