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A pair of prominent opponents of President Trump secured significant legal victories on the start of the week when a federal judge dismissed the federal indictments against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are innocent, claiming that the administration and DOJ are merely targeting them for revenge.

Federal Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. However, she left the door open for the federal authorities to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have compromised Comey case
• What is ex-FBI director 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 seemed to confirm it: This will not be the final word on this issue.

But the DOJ confronts significant obstacles to successfully prosecute either after this defeat, and legal analysts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, said Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

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

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

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

Abbe Lowell, James's lawyer, pledged to continue to challenge any additional politically driven indictments through all legal avenues.

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

Is it possible there be new charges?

The government charged James 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, they also asserted to be victims of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the government might try to convene fresh grand juries and obtain new indictments.

Based on my analysis, a new prosecutor could bring James' case to a different grand jury and get a fresh indictment, stated Ms Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

It's clear that it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is able to secure an indictment.

He described the complex web of lawyers, judges, and motions involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to file the exact same charges against James Comey.

One problem is the statute of limitations – the time frame that government lawyers had to indict 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 bring the case again.

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

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

What happens to prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

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

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

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

That leaves Halligan's position on future cases against both individuals, once more, unclear.

The ruling also could cast a shadow on any other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

But Bondi said on Monday that she made Halligan a special federal prosecutor and commended her work as outstanding.

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.