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Two well-known critics of President Trump obtained significant court wins on Monday when a federal judge dismissed the federal indictments filed against them.

For weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are simply singling out them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. But she also left open the possibility for the government to refile the case.

• Judge dismisses charges against ex-FBI director Comey and NY attorney general James
• Federal judge states DOJ errors may have compromised the Comey trial
• What is ex-FBI director James Comey accused of?

Comey admitted that likelihood after the ruling, saying he believes Trump is likely to come after him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this matter.

But the DOJ faces significant hurdles to successfully prosecute both after this defeat, and legal analysts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

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

Might the DOJ challenge the ruling?

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

US Attorney General Pam Bondi signaled she would take this route, vowing to use all available legal action, including an expedited appeal.

Previously, the Trump administration has strongly challenged adverse decisions, moving cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically motivated charges through all legal avenues.

If there is an appeals process, the justice department likely would have its own lawyers argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be fresh indictments?

The government accused James Comey with making false statements to lawmakers and obstructing justice. Federal prosecutors charged James with financial fraud and providing false information to a bank.

Both pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, they also claimed to be victims of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the government might try to convene new grand juries and secure new indictments.

Based on my analysis, a different attorney could bring James' case to a different grand jury and get a fresh indictment, said 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.

It's clear that it will be strongly disputed, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is can obtain an charge.

He characterized the tangle of attorneys, judges, and legal filings involved as a legal quagmire with no simple answers.

It might be harder for the DOJ to try to file the identical accusations against James Comey.

A key issue is the statute of limitations – the deadline that prosecutors had to indict Comey for these specific allegations – which expired at the close of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to bring the case again.

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

The ruling also suggests that because the charge is void, the time limit has expired and there can be no new indictment, lawyer Patrick Fitzgerald said 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 appoint Ms. Halligan as Acting US Attorney for the Virginia Eastern District was unlawful.

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

Federal prosecutors are nominated by the US president and require Senate approval. Federal statutes regulate how individuals can be assigned on a temporary basis, but the judge determined that Halligan's assignment had breached these laws.

That leaves Halligan's position on subsequent cases against both individuals, again, unclear.

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

But Bondi said on Monday that she designated her a special federal prosecutor 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.