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Two high-profile critics of President Trump obtained major court wins on the start of the week when a US judge threw out the federal indictments against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are innocent, claiming that the administration and DOJ are merely singling out them for revenge.

Federal Judge Cameron Currie tossed the indictments in their cases due to attorney Lindsey Halligan's improper appointment as federal prosecutor. However, she left open the possibility for the government to try again.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• US judge says DOJ errors may have tainted Comey case
• What are ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the decision, stating 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 final word on this issue.

But the DOJ confronts steep obstacles to effectively try either after this setback, and experts are reluctant to predict what could occur next due to the cases' unprecedented nature.

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

Might the justice department challenge the ruling?

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

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

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

Abbe Lowell, James's lawyer, vowed to continue to challenge any additional politically motivated charges through all legal avenues.

If there is an appeals process, the DOJ likely would have its own lawyers argue the case, making Halligan's involvement in the appeals process uncertain.

Could there be new charges?

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

Each entered not guilty pleas. Besides claiming Halligan was unlawfully appointed, both 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.

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

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

I can tell you it will be hotly contested, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He characterized the complex web of attorneys, courts, and motions involved as a legal quagmire with no simple answers.

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

One problem is the statute of limitations – the time frame that government lawyers had to charge Comey for these particular claims – which expired at the close of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department to refile the case.

Still in that case, his legal team said it plans to argue the government is past the deadline.

The ruling also suggests that since the charge is void, the statute of limitations has run and there can be no new indictment, lawyer 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, Judge Currie was blunt: Halligan's appointment was improper.

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

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

US attorneys are proposed by the president and require US Senate confirmation. 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 role on future cases against both individuals, again, unclear.

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

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

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