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A pair of prominent critics of President Trump obtained major court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

For weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, claiming that the administration and DOJ are simply singling out them for retaliation.

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

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Comey admitted that possibility after the ruling, stating he believes the former president is likely to come after him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This isn't the final word on this issue.

But the DOJ faces steep hurdles to effectively try both after this setback, and experts hesitate to forecast what could occur next due to the unprecedented circumstances of the cases.

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

Might the DOJ 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.

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

In other cases, the former administration has strongly challenged unfavourable rulings, taking cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically motivated charges through all legal avenues.

In the event of an appeal, the DOJ probably would have its own attorneys argue the case, making Halligan's role in the appeal unclear.

Could there be new charges?

The government accused James Comey with lying to Congress and obstructing justice. Government lawyers charged James with bank fraud and making false statements to a bank.

Each entered not guilty pleas. In addition to 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 DOJ might try to assemble new grand juries and obtain new indictments.

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

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

I can tell you it will be hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is can obtain an indictment.

He described the complex web of lawyers, courts, and motions involved as a procedural morass with no simple answers.

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

A key issue is the statute of limitations – the deadline that prosecutors had to indict him for these particular claims – which expired at the end of September. However, the indictment's dismissal would activate a six-month grace period for the justice department to refile the case.

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

The ruling also suggests that since the indictment is invalid, the statute of limitations has expired and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

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

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

US attorneys are nominated by the US president and need US Senate confirmation. Federal statutes regulate how individuals can be appointed on a temporary basis, but the judge determined that Halligan's assignment had violated these regulations.

That leaves Halligan's role on subsequent cases against James and Comey, once more, unclear.

The decision might also raise doubts on other cases Halligan has prosecuted in the Virginia Eastern District where she works.

But Attorney General Bondi said on that day that she designated Halligan a special federal prosecutor and commended her work as excellent.

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