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

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have argued fiercely that they are innocent, asserting that the president and justice department are simply targeting them for revenge.

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

• Judge dismisses charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that likelihood after the decision, stating 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 last chapter on this issue.

But the DOJ confronts steep hurdles to effectively try both 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, stated Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

The Department of Justice can challenge Judge Currie's ruling before a higher appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

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

In other cases, the former administration has aggressively appealed unfavourable rulings, moving cases from lower courts and sometimes accelerating its petitions up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically driven indictments through every lawful means available.

In the event of an appeal, the justice department likely would have its own attorneys present the arguments, making Halligan's role in the appeal uncertain.

Could there be new charges?

The federal prosecutors charged Comey with lying to Congress and obstruction of justice. Federal prosecutors charged James with financial fraud and providing false information to a bank.

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, 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 new grand juries and obtain new charges.

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

But legal expert 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 recharged if a lawfully appointed prosecutor is assigned and is can obtain an charge.

He characterized the complex web of attorneys, courts, and legal filings 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 Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to indict him for these particular claims – which ended at the end of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to refile the case.

Still in that situation, his lawyers said it plans to argue the government is out of time.

The decision further indicates that since the indictment is invalid, the time limit has expired and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of 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 AG's effort to appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was invalid.

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

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

That leaves Halligan's role on subsequent cases against both individuals, once more, uncertain.

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

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

The White House maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.