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Two high-profile critics of former President Trump obtained major court wins on Monday when a US judge threw out the federal indictments filed against them.

For weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, asserting that the administration and DOJ are simply targeting them for retaliation.

Federal Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the federal authorities to refile the case.

• Court throws out cases against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have tainted the Comey trial
• What is former FBI head James Comey charged with?

Comey acknowledged that possibility after the decision, saying he thinks Trump will probably come after him once more.

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

But the DOJ confronts steep obstacles to successfully prosecute both after this setback, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

The Department of Justice can challenge the judge's decision before a higher appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

In other cases, the former administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes fast-tracking its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically motivated charges through every lawful means available.

In the event of an appeal, the DOJ probably would have its own attorneys argue the case, making Halligan's role in the appeals process uncertain.

Is it possible there be fresh indictments?

The federal prosecutors accused James Comey with making false statements to lawmakers and obstructing justice. Government lawyers indicted Letitia James with financial fraud and making false statements to a bank.

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, both also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the government might try to convene fresh 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, said Ms Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

It's clear that it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

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

It could be harder for the government to try to file the exact same charges against James Comey.

One problem is the legal time limit – the deadline that prosecutors had to charge Comey for these specific allegations – which expired at the end of September. However, the indictment's dismissal would trigger a half-year extension for the justice department to bring the case again.

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

The decision further indicates that since the charge is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

The judge stated in the James decision that the AG's effort to install Halligan as Interim US Attorney for the Eastern District of Virginia was unlawful.

Therefore, she lacked legal power to file the charges, the judge wrote.

US attorneys are proposed by the president and require Senate approval. US laws regulate how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's appointment had breached these laws.

That leaves Halligan's position on subsequent cases against James and Comey, again, uncertain.

The ruling also could cast a shadow on other cases Halligan has brought in the Virginia Eastern District where she serves.

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

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