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Two prominent opponents of former President Trump achieved significant court wins on Monday when a US 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 fiercely that they are not guilty, asserting that the president and justice department are merely singling out them for retaliation.

US District Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. However, she left the door open for the federal authorities to try again.

• Court throws out cases against ex-FBI director Comey and New York AG James
• US judge says government 'missteps' may have tainted Comey case
• What are ex-FBI director James Comey charged with?

Comey acknowledged that likelihood after the ruling, saying he believes Trump will probably target him again.

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

But the DOJ faces steep obstacles to successfully prosecute either after this defeat, and experts hesitate to forecast what could happen next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, stated Kay Levine, Emory University School of Law professor.

Could the DOJ appeal?

The Department of Justice can challenge 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 indicated she would take this route, vowing to use all available legal action, including an expedited appeal.

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

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

In the event of an appeals process, the DOJ probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal unclear.

Could there be fresh indictments?

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

Each pleaded not guilty. Besides claiming 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 convene new grand juries and secure new charges.

As far as everything I've seen, a different attorney could present James's case to a new grand jury and get a fresh indictment, said Professor Levine.

But John Day, head of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is able to secure an indictment.

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

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 dismissal of the charges would activate a half-year extension for the DOJ to refile the case.

Even so in that situation, his lawyers said it intends to argue the government is past the deadline.

The decision further indicates that because 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 blunt: Halligan's appointment was improper.

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

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

Federal prosecutors are nominated by the US president and need Senate approval. Federal statutes govern how people can be assigned on a interim basis, but the judge determined that Halligan's appointment had violated these laws.

This makes Halligan's role on subsequent cases against James and Comey, once more, uncertain.

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

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

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