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Two well-known critics of President Trump obtained significant court wins on Monday when a US judge threw out the government's charges filed against them.

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

US District Judge Cameron Currie dismissed the charges against them due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. But she also left the door open for the federal authorities to refile the case.

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Comey admitted that likelihood after the ruling, saying he thinks the former president is likely to target him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the DOJ faces steep obstacles to successfully prosecute both after this defeat, and experts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, said Kay Levine, law professor at Emory University.

Could the justice department appeal?

The DOJ can contest 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, pledging to use all legal means, including an immediate 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, pledged to continue to challenge any further politically driven indictments through every lawful means available.

In the event of an appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's role in the appeal uncertain.

Could there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to lawmakers and obstruction of justice. Government lawyers charged James with bank fraud and making false statements to a financial institution.

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

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

Based on my analysis, a new prosecutor could present James's case to a new grand jury and get a fresh indictment, said Ms Levine.

But legal expert 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 strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He characterized the complex web of attorneys, courts, and legal filings involved as a procedural morass with no simple answers.

It might be harder for the DOJ to try to bring the exact same charges against James Comey.

One problem is the legal time limit – the deadline that government lawyers had to indict Comey for these specific allegations – which ended at the end of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the justice department to bring the case again.

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

The ruling also suggests that since the indictment is void, the time limit has run and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

Judge Currie wrote 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 file the charges, the judge wrote.

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

This makes Halligan's position on subsequent cases against James and Comey, again, uncertain.

The decision might also cast a shadow on other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

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

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.