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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 federal indictments against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are simply targeting them for revenge.

Federal Judge Cameron Currie dismissed the indictments in their cases due to attorney Lindsey Halligan's improper assignment as US attorney. But she also left open the possibility for the government to try again.

• Court throws out charges against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have tainted the Comey trial
• What are ex-FBI director James Comey accused of?

Comey acknowledged that likelihood after the ruling, stating he believes Trump is likely to target him once more.

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

But the government faces steep hurdles to successfully prosecute both after this setback, and legal analysts hesitate to forecast what could happen next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, stated Kay Levine, law professor at Emory University.

Might the DOJ challenge the ruling?

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

US Attorney General Pam Bondi signaled she would take this route, pledging to use all legal means, including an immediate appeal.

Previously, the Trump administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, James's lawyer, pledged to keep fighting any additional politically motivated charges through every lawful means available.

If there is an appeals process, the justice department probably would have its own lawyers argue the case, making Halligan's involvement in the appeals process uncertain.

Could there be new charges?

The government charged James Comey with lying to lawmakers and obstructing justice. Government lawyers charged James with bank fraud and providing false information to a financial institution.

Both entered not guilty pleas. In addition to arguing Halligan's appointment was invalid, they also asserted to be targets of vindictive prosecution.

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

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 Ms Levine.

But 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 properly assigned attorney is assigned and is able to secure an indictment.

He described the tangle of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

It could be harder for the government to try to file the identical accusations against James Comey.

One problem is the legal time limit – the deadline that government lawyers had to charge him for these specific allegations – which ended at the end of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the DOJ to refile the case.

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

The decision further indicates that because the indictment is invalid, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

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

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

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

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

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

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

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.