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A pair of high-profile opponents of President Trump achieved major court wins on Monday when a federal judge threw out the government's charges against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have argued vehemently that they are not guilty, claiming that the president and justice department are merely targeting them for retaliation.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. However, she left the door open for the federal authorities to try again.

• Judge dismisses cases against former FBI chief Comey and NY attorney general James
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• What are former FBI head James Comey accused of?

Comey acknowledged that likelihood after the ruling, saying he thinks the former president will probably target him once more.

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

But the government confronts significant hurdles to successfully prosecute either after this defeat, and experts hesitate to predict what could occur next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Professor Kay Levine, Emory University School of Law professor.

Could the DOJ challenge the ruling?

The DOJ 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, pledging to use all available legal action, including an immediate appeal.

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

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any further 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 involvement in the appeals process unclear.

Could there be new charges?

The federal prosecutors accused James Comey with lying to Congress and obstruction of justice. Government lawyers charged James with bank fraud and making false statements to a bank.

Each entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, both also claimed to be targets of vindictive prosecution.

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

As far as everything I've seen, a new prosecutor could bring James' case to a new grand jury and get a new indictment, stated Professor Levine.

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

I can tell you it will be strongly disputed, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He characterized the tangle of lawyers, judges, and legal filings involved as a procedural morass with no easy solutions.

It might be more difficult for the government to try to bring the identical accusations against James Comey.

A key issue is the legal time limit – the deadline that prosecutors had to charge him for these specific allegations – which expired at the end of September. However, the indictment's dismissal would activate a half-year extension for the justice department to refile the case.

Still in that situation, his legal team said it intends to argue the government is past the deadline.

The decision further indicates that because the charge is void, the time limit has run 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 indictments 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 appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

Therefore, she had no lawful authority to file the charges, she wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. US laws regulate how people can be appointed on a interim basis, but Judge Currie found that Halligan's appointment had breached these regulations.

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

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

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

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