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A pair of well-known opponents of President Trump obtained significant court wins on the start of the week when a federal judge threw out the government's charges against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have argued vehemently that they are innocent, asserting that the president and justice department are merely singling out them for revenge.

US District Judge Cameron Currie dismissed the charges against them due to attorney Lindsey Halligan's invalid assignment as US attorney. But she also left the door open for the government to refile the case.

• Court throws out cases against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have compromised the Comey trial
• What is former FBI head James Comey charged with?

Comey acknowledged that likelihood after the decision, saying he thinks the former president will probably come after him once more.

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

But the government confronts steep hurdles to effectively try both after this defeat, and experts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, stated Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

The DOJ can challenge the judge's decision before a federal appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

Previously, the Trump administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically driven indictments through all legal avenues.

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.

Is it possible there be new charges?

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

Each pleaded not guilty. Besides claiming Halligan was unlawfully appointed, they 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 charges.

Based on my analysis, a new prosecutor could present James's 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 the Comey matter.

I can tell you it will be strongly disputed, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is able to secure an charge.

He described the complex web of lawyers, judges, and legal filings involved as a procedural morass with no easy solutions.

It could be more difficult for the DOJ to try to bring the identical accusations against Comey.

One problem is the statute of limitations – the deadline that government lawyers had to charge him for these particular claims – which ended at the close of September. Nonetheless, the dismissal of the charges would activate a half-year extension for the DOJ to bring the case again.

Still in that situation, his legal team said it plans to argue the prosecution is out of time.

The ruling also suggests that since the charge is invalid, 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 both decisions on the indictments 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 appoint Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

Therefore, she had no lawful authority to present the indictment, the judge wrote.

US attorneys are nominated by the president and need Senate approval. US laws govern how people can be assigned on a interim basis, but Judge Currie found that Halligan's appointment had breached these laws.

That leaves Halligan's role on future cases against James and Comey, again, uncertain.

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

But Attorney General Bondi said on that day that she designated her a special US attorney and praised her work as excellent.

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