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Two well-known critics of former President Trump achieved significant court wins on the start of the week when a federal judge dismissed the federal indictments filed against them.

For weeks following their charges, 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 simply singling out them for revenge.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the government to refile the case.

• Judge dismisses cases against ex-FBI director Comey and New York AG James
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• What are ex-FBI director James Comey charged with?

Comey admitted that possibility after the ruling, stating he thinks Trump is likely to come after him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this matter.

But the DOJ faces significant hurdles to successfully prosecute both after this defeat, and experts are reluctant to predict what could occur next due to the cases' unprecedented nature.

In my view, it's uncharted territory, said Kay Levine, law professor at Emory University.

Might the DOJ appeal?

The Department of Justice 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, pledging to use all available legal action, including an immediate appeal.

In other cases, the Trump administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to keep fighting any further politically driven indictments through every lawful means available.

If there is an appeal, the justice department probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal uncertain.

Could there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstruction of justice. Government lawyers indicted James with bank fraud and making false statements to a financial institution.

Both entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, they also claimed to be targets of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to assemble fresh grand juries and secure new charges.

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

It's clear that it will be strongly disputed, whether Mr Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an charge.

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

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

One problem is the legal time limit – the deadline that government lawyers had to charge Comey for these particular claims – which ended at the end of September. Nonetheless, the indictment's dismissal would activate a half-year extension for the DOJ to bring the case again.

Still in that case, his legal team said it intends to contend the government is out of time.

The ruling also suggests that since the charge is invalid, the time limit has expired and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

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

The judge stated in the James ruling that the Attorney General's attempt to install Ms. Halligan as Acting US Attorney for the Virginia Eastern District was unlawful.

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

US attorneys are nominated by the president and require US Senate confirmation. US laws regulate how individuals can be appointed on a interim basis, but the judge determined that Halligan's appointment had breached these regulations.

That leaves Halligan's role on future cases against both individuals, again, unclear.

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

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

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.