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Two prominent opponents of President Trump secured major court wins on the start of the week when a federal judge threw out the government's charges against them.

Over recent weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently that they are not guilty, asserting that the president and justice department are simply targeting them for revenge.

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

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Comey acknowledged that likelihood after the ruling, saying he believes the former president is likely to come after him again.

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

But the government confronts steep hurdles to effectively try both after this defeat, and experts hesitate to forecast what could occur next due to the cases' unprecedented nature.

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

Might the DOJ appeal?

The DOJ can contest 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 signaled she would pursue this option, vowing to use all available legal action, including an immediate appeal.

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

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

If there is an appeals process, the justice department probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal uncertain.

Could there be new charges?

The federal prosecutors accused Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted James with financial fraud and providing false information to a financial institution.

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

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to convene fresh grand juries and secure new indictments.

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

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

I can tell you it will be strongly disputed, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is able to secure an indictment.

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

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

A key issue is the legal time limit – the deadline that government lawyers had to charge Comey for these specific allegations – which expired at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department to refile the case.

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

The ruling also suggests that because the indictment is void, the statute of limitations has run and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against James and Comey, the judge was direct: Halligan was wrongly appointed.

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

As a result, Halligan lacked legal power to file the charges, she wrote.

US attorneys are nominated by the US president and need US Senate confirmation. Federal statutes 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 position on future cases against James and Comey, once more, 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 Halligan a special US attorney and praised her work as excellent.

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