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A pair of prominent critics of President Trump secured significant court wins on the start of the week when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted vehemently that they are not guilty, claiming that the president and justice department are simply targeting them for revenge.

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

• Court throws out charges against former FBI chief Comey and New York AG James
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Comey admitted that possibility after the ruling, saying he thinks the former president will probably come after him once more.

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

But the DOJ confronts significant obstacles to successfully prosecute either 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 Professor Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

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

Attorney General Pam Bondi indicated she would pursue this option, vowing to use all legal means, including an immediate appeal.

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

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically motivated charges through all legal avenues.

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

Could there be new charges?

The federal prosecutors charged Comey with lying to Congress and obstructing justice. Federal prosecutors charged James with bank fraud and providing false information to a bank.

Both entered not guilty pleas. In addition to claiming Halligan's appointment was invalid, both also claimed to be victims of vindictive prosecution.

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

As far as everything I've seen, a new prosecutor could present James's case to a different grand jury and get a fresh indictment, stated Ms Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – especially in Comey's case.

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is can obtain an charge.

He described the complex web of lawyers, judges, and legal filings involved as a legal quagmire with no easy solutions.

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

One problem is the legal time limit – the deadline that government lawyers had to indict 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 DOJ to bring the case again.

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

The decision further indicates that because the charge is invalid, 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 the pair of rulings on the charges against James and Comey, Judge Currie was blunt: Halligan was wrongly appointed.

The judge stated in the James ruling that the AG's effort to appoint Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

Therefore, Halligan had no lawful authority to present the indictment, she wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. US laws govern how individuals can be appointed on a temporary basis, but the judge determined that Halligan's appointment had breached these regulations.

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

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

But Bondi said on Monday that she made Halligan a special federal prosecutor and commended her work as excellent.

The White House stood by its stance that Halligan's appointment was legal, press secretary Karoline Leavitt told the press on Monday.