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A pair of prominent opponents of former President Trump secured major court wins on Monday when a federal judge threw out the federal indictments against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have insisted fiercely that they are innocent, claiming that the president and justice department are merely targeting them for retaliation.

Federal Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid appointment as federal prosecutor. However, she left the door open for the government to refile the case.

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Comey acknowledged that possibility after the decision, stating he thinks Trump will probably target him once more.

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

But the DOJ faces significant hurdles to effectively try either after this defeat, and experts are reluctant to forecast what could happen next due to the cases' unprecedented nature.

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

Could the DOJ appeal?

The DOJ can contest 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 signaled she would take this route, pledging to use all available legal action, including an immediate appeal.

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

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

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

Could there be new charges?

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

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

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

As far as everything I've seen, a different attorney could bring James' case to a different grand jury and secure a fresh indictment, stated Professor Levine.

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

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 able to secure an charge.

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

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 government lawyers had to indict Comey for these specific allegations – which ended at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the DOJ to refile the case.

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

The ruling also suggests that because the indictment is void, the time limit has expired and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

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

As a result, she lacked legal power to present the indictment, she wrote.

Federal prosecutors are nominated by the US president and require Senate approval. Federal statutes regulate how individuals can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had violated these laws.

This makes Halligan's position on subsequent cases against both individuals, again, unclear.

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

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

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