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A pair of prominent critics of President Trump obtained significant legal victories on the start of the week when a US judge threw out the government's charges filed against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have insisted fiercely that they are innocent, claiming that the president and justice department are simply singling out them for revenge.

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

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Comey admitted that possibility after the decision, saying he believes the former president is likely to target him again.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the final word on this matter.

But the DOJ faces steep obstacles to effectively try either after this defeat, and experts hesitate to predict what could occur next due to the cases' unprecedented nature.

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

Might the DOJ appeal?

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

US 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 strongly challenged adverse decisions, moving cases from lower courts and sometimes accelerating 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.

In the event of an appeal, the DOJ probably would have its own attorneys present the arguments, making Halligan's role in the appeal unclear.

Could there be fresh indictments?

The government charged James Comey with lying to lawmakers and obstruction of justice. Government lawyers charged James with bank fraud and providing false information to a bank.

Both pleaded not guilty. Besides arguing Halligan was unlawfully appointed, both also asserted to be victims 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 secure new charges.

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

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

I can tell you it will be strongly disputed, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an charge.

He described the complex web of attorneys, judges, and motions involved as a procedural morass with no easy solutions.

It might 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 time frame that government lawyers had to indict Comey for these particular claims – which expired at the close of September. However, the dismissal of the charges would trigger a six-month grace period for the DOJ to refile the case.

Still in that situation, his lawyers said it intends to argue the prosecution is past the deadline.

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

What happens to prosecutor Lindsey Halligan?

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

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

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

Federal prosecutors are proposed by the president and need Senate approval. US laws regulate how individuals can be appointed on a temporary basis, but the judge determined that Halligan's assignment had violated these laws.

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

The ruling also could cast a shadow on any other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

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

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