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A pair of high-profile critics of President Trump secured major court wins on Monday when a federal judge threw out the federal indictments against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have argued fiercely that they are innocent, asserting that the administration and DOJ are simply singling out them for revenge.

Federal Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's improper assignment as US attorney. But she also left the door open for the government 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 seemed to confirm it: This will not be the last chapter on this matter.

But the government faces significant hurdles to successfully prosecute both after this setback, and experts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

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

Could the DOJ appeal?

The Department of Justice can challenge 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 indicated she would take this route, vowing to use all available legal action, including an immediate appeal.

Previously, the former administration has aggressively appealed adverse decisions, moving cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically driven indictments through every lawful means available.

If there is an appeal, the justice department likely would have its own attorneys present the arguments, making Halligan's role in the appeal unclear.

Could there be new charges?

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

Each entered not guilty pleas. In addition to arguing Halligan's appointment was invalid, both also claimed to be targets of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to convene fresh grand juries and secure new charges.

Based on my analysis, a new prosecutor could bring James' case to a different grand jury and get a new indictment, stated Ms Levine.

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

I can tell you it will be strongly disputed, whether Mr Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an indictment.

He characterized the tangle of attorneys, courts, and motions involved as a legal quagmire with no easy solutions.

It could be harder for the DOJ to try to file the identical accusations against Comey.

One problem is the legal time limit – the deadline that prosecutors had to indict him for these specific allegations – which expired at the end of September. However, 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 legal team said it intends to contend the government is out of time.

The decision further indicates that since the indictment is void, the time limit has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

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

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

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

Federal prosecutors are nominated by the president and need US Senate confirmation. Federal statutes regulate how individuals can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had violated these laws.

This makes Halligan's position on future cases against James and Comey, once more, uncertain.

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

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

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