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Two high-profile opponents of President Trump achieved major court wins on Monday when a federal judge threw out the federal indictments against them.

For weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have maintained fiercely that they are not guilty, asserting that the president and justice department are merely targeting them for retaliation.

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

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Comey admitted that likelihood after the decision, stating he believes the former president will probably target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the last chapter on this matter.

But the government faces steep obstacles to successfully prosecute either after this defeat, and legal analysts hesitate to predict what could happen next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Professor 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 case, that would be the Fourth Circuit Appeals Court.

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

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

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

In the event of an appeal, the DOJ probably would have its own attorneys argue the case, making Halligan's role in the appeals process uncertain.

Could there be new charges?

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

Each pleaded not guilty. Besides arguing Halligan was unlawfully appointed, they also asserted to be targets of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the government might try to convene fresh grand juries and obtain new indictments.

Based on my analysis, a different attorney could present James's case to a different grand jury and get a fresh indictment, said Ms Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complex process – especially in the Comey matter.

I can tell you it will be hotly contested, whether Comey's case can be recharged if a properly assigned attorney is appointed and is can obtain an charge.

He characterized the complex web of lawyers, courts, and motions involved as a procedural morass with no easy solutions.

It could be harder for the DOJ to try to bring the exact same charges against Comey.

One problem is the statute of limitations – the deadline that prosecutors had to charge Comey for these specific allegations – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the DOJ to bring the case again.

Even so in that situation, his lawyers said it plans to contend the prosecution is past the deadline.

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

What is the fate of Lindsey Halligan?

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

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

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

Federal prosecutors are nominated by the US 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 violated these regulations.

This makes Halligan's role on future cases against James and Comey, once more, unclear.

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

But Bondi said on that day that she made her a special federal prosecutor and praised her work as excellent.

The White House stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.