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Two high-profile opponents of President Trump secured major court wins on Monday when a federal judge threw out the government's charges filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, claiming that the administration and DOJ are merely singling out them for revenge.

US District Judge Cameron Currie tossed the indictments against them due to prosecutor Lindsey Halligan's invalid assignment as US attorney. But she also left open the possibility for the federal authorities to refile the case.

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Comey acknowledged that possibility after the decision, saying he thinks the former president is likely to target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the last chapter on this issue.

But the government confronts significant hurdles to successfully prosecute either after this setback, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Professor Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

The DOJ can contest the judge's decision before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

US Attorney General Pam Bondi signaled she would take this route, pledging 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 petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically motivated charges through every lawful means available.

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

Is it possible there be fresh indictments?

The government accused James Comey with lying to lawmakers and obstruction of justice. Federal prosecutors charged James with financial fraud and making false statements to a financial institution.

Both pleaded not guilty. Besides claiming Halligan's appointment was invalid, both also asserted to be victims of vindictive prosecution.

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

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

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

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

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

It might be more difficult for the DOJ to try to bring the identical accusations against Comey.

A key issue is the statute of limitations – the deadline that prosecutors had to charge him for these particular claims – which ended 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.

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

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

What is the fate of prosecutor Lindsey Halligan?

In both decisions on the charges against James and Comey, Judge Currie was direct: Halligan was wrongly appointed.

The judge stated in the James ruling that the Attorney General's attempt to install Ms. Halligan as Acting US Attorney for the Virginia Eastern District was unlawful.

As a result, Halligan had no lawful authority to file the charges, she wrote.

Federal prosecutors are proposed by the US president and need Senate approval. Federal statutes govern how people can be appointed on a interim basis, but Judge Currie found that Halligan's assignment had violated these laws.

This makes Halligan's position on future cases against both individuals, again, uncertain.

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

But Attorney General Bondi said on that day that she made Halligan a special US attorney and praised her work as outstanding.

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