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A pair of high-profile opponents of President Trump obtained significant legal victories on the start of the week when a US judge threw out the government's charges filed against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted fiercely that they are not guilty, asserting that the president and justice department are merely targeting 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 government to try again.

• Court throws out cases against former FBI chief Comey and NY attorney general James
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Comey acknowledged that likelihood 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 government faces steep hurdles to effectively try both after this defeat, and legal analysts hesitate to forecast what could happen next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, stated Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

The DOJ can contest the judge's decision before a federal appeals court. In this instance, 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 expedited appeal.

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

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

If there is an appeals process, the justice department likely would have its own lawyers present the arguments, making Halligan's involvement in the appeal uncertain.

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 bank fraud and making false statements to a financial institution.

Both pleaded not guilty. Besides claiming Halligan's appointment was invalid, they also claimed to be victims of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the government might try to assemble new grand juries and obtain new charges.

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

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

I can tell you 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 charge.

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 DOJ to try to bring the exact same charges against Comey.

One problem is the legal time limit – the deadline that prosecutors had to charge Comey for these particular claims – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a six-month grace period for the justice department to refile the case.

Still in that situation, his legal team said it plans to contend the prosecution is past the deadline.

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

What is the fate of prosecutor Lindsey Halligan?

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

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

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

Federal prosecutors are proposed by the US president and need Senate approval. US laws regulate how individuals can be assigned on a interim basis, but the judge determined that Halligan's assignment had breached these regulations.

That leaves Halligan's position on subsequent cases against both individuals, once more, uncertain.

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

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

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