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A pair of high-profile opponents of former President Trump achieved significant court wins on the start of the week when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued fiercely that they are innocent, claiming that the administration and DOJ are merely singling out them for retaliation.

US District Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. But she also left open the possibility for the government to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that possibility after the decision, saying he thinks Trump will probably come after him again.

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

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

It feels to me like uncharted territory, stated Professor Kay Levine, law professor at Emory University.

Might the justice department challenge the ruling?

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

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

In other cases, the Trump administration has aggressively appealed unfavourable rulings, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically motivated charges through every lawful means available.

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

Could there be fresh indictments?

The federal prosecutors accused Comey with making false statements to lawmakers and obstruction of justice. Government lawyers charged Letitia James with financial fraud and providing false information to a bank.

Each entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, both also claimed to be targets of retaliatory legal action.

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

As far as everything I've seen, a new prosecutor 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 – especially in Comey's case.

It's clear that it will be strongly disputed, 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 lawyers, judges, and legal filings involved as a procedural morass with no simple answers.

It might be harder for the DOJ to try to file the exact same charges against James Comey.

One problem is the legal time limit – the deadline that prosecutors had to indict him for these specific allegations – which expired at the close of September. However, the indictment's dismissal would trigger a half-year extension for the justice department to refile the case.

Even so in that situation, his legal team said it intends to contend the prosecution is past the deadline.

The ruling also suggests that because the indictment 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 charges against Comey and James, the judge was direct: Halligan's appointment was improper.

Judge Currie wrote in the James decision that the AG's effort to install Halligan as Interim US Attorney for the Eastern District of Virginia was unlawful.

As a result, she lacked legal power to file the charges, she wrote.

US attorneys are proposed by the president and need Senate approval. Federal statutes govern how individuals can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had violated these laws.

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

The decision might also raise doubts on other cases Halligan has brought in the Eastern District of Virginia where she serves.

But Bondi said on Monday that she made Halligan a special US attorney and commended her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.