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A pair of high-profile opponents of former President Trump obtained major legal victories on Monday when a federal judge threw out the federal indictments filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained fiercely that they are not guilty, asserting that the administration and DOJ are simply targeting them for revenge.

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

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Comey admitted that likelihood after the decision, saying he believes Trump is likely to target him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the final word on this matter.

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

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

Might the justice department challenge the ruling?

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.

US Attorney General Pam Bondi signaled she would pursue this option, pledging to use all available legal action, including an expedited appeal.

In other cases, the Trump administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

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

If there is an appeals process, the DOJ probably would have its own lawyers present the arguments, making Halligan's involvement in the appeals process unclear.

Could there be fresh indictments?

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

Both pleaded not guilty. In addition to claiming Halligan's appointment was invalid, both also claimed to be targets of retaliatory legal action.

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

Based on my analysis, a different attorney could bring James' case to a different grand jury and get a fresh indictment, said Professor Levine.

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

It's clear that it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an charge.

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

It could be more difficult for the DOJ to try to file the identical accusations against James Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to indict him for these specific allegations – which ended at the end of September. However, the dismissal of the charges would activate a half-year extension for the justice department to bring the case again.

Even so in that case, his lawyers said it intends to contend the government is out of time.

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

What happens to Lindsey Halligan?

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

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

As a result, Halligan lacked legal power to present the indictment, the judge wrote.

US attorneys are nominated by the president and need US Senate confirmation. Federal statutes regulate how individuals can be appointed on a interim basis, but Judge Currie found that Halligan's appointment had breached these laws.

This makes Halligan's role on future cases against James and Comey, again, unclear.

The decision might also raise doubts on any other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

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

The administration stood by its stance that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.