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A pair of high-profile critics of former President Trump obtained significant court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are not guilty, asserting that the president and justice department are simply targeting them for revenge.

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

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Comey admitted that possibility after the decision, stating he thinks the former president is likely to target him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the last chapter on this matter.

But the government faces significant obstacles to successfully prosecute both after this defeat, and legal analysts hesitate to predict what could happen next due to the cases' unprecedented nature.

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

Could the justice department appeal?

The Department of Justice can challenge Judge Currie's ruling 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 expedited appeal.

Previously, the former administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes fast-tracking its petitions up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically motivated charges through every lawful means available.

In the event of an appeals process, the justice department likely would have its own attorneys argue the case, making Halligan's role in the appeal unclear.

Is it possible there be fresh indictments?

The government accused Comey with making false statements to Congress and obstruction of justice. Federal prosecutors indicted Letitia James with financial fraud and making false statements to a financial institution.

Both pleaded not guilty. In addition to claiming Halligan's appointment was invalid, they also claimed to be victims of retaliatory legal action.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to convene new grand juries and obtain new charges.

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and get a new indictment, said Professor Levine.

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

It's clear that 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 charge.

He characterized the tangle of lawyers, courts, and motions involved as a legal quagmire with no simple answers.

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

A key issue is the legal time limit – the time frame that prosecutors had to charge Comey for these particular claims – which expired at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to bring the case again.

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

The decision further indicates that because the charge 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 prosecutor Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, the judge was blunt: Halligan was wrongly appointed.

Judge Currie wrote in the James decision that the Attorney General's attempt to install Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

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

Federal prosecutors are proposed by the president and require Senate approval. Federal statutes govern how people can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had violated these regulations.

That leaves Halligan's position on future cases against James and Comey, once more, uncertain.

The ruling also could raise doubts on other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

But Bondi said on Monday that she made her a special US attorney and praised her work as outstanding.

The administration maintained its position that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.