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Two prominent opponents of President Trump achieved major legal victories on the start of the week when a federal judge threw out the federal indictments against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have maintained vehemently that they are not guilty, asserting that the president and justice department are merely singling out them for revenge.

Federal Judge Cameron Currie dismissed the charges against them due to attorney 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, stating he believes Trump is likely to target him again.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the final word on this matter.

But the DOJ confronts significant hurdles to effectively try either after this setback, and experts hesitate to forecast what could happen next due to the unprecedented circumstances of the cases.

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

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 Appeals Court.

Attorney General Pam Bondi signaled she would take this route, vowing to use all legal means, including an immediate 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 Supreme Court.

Abbe Lowell, James's lawyer, vowed to continue to challenge any further politically driven indictments 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 involvement in the appeal uncertain.

Is it possible there be new charges?

The government accused James Comey with lying to lawmakers and obstructing justice. Government lawyers indicted 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, they also asserted to be victims of retaliatory legal action.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to convene fresh grand juries and obtain new charges.

Based on my analysis, a different attorney could bring James' case to a new grand jury and secure a new indictment, said Ms Levine.

But legal expert 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 hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an charge.

He described the tangle of attorneys, 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 James Comey.

A key issue is the legal time limit – the time frame that government lawyers had to charge him for these specific allegations – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a half-year extension for the DOJ to refile the case.

Even so in that situation, his legal team said it intends to contend the prosecution is out of time.

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

What is the fate of prosecutor Lindsey Halligan?

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

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

Therefore, she lacked legal power to file the charges, 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 assignment had violated these regulations.

That leaves Halligan's position on subsequent cases against James and Comey, once more, unclear.

The decision might also raise doubts on other cases Halligan has brought in the Virginia Eastern District where she works.

But Bondi said on Monday that she designated her a special US attorney and praised her work as excellent.

The administration stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.