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Two prominent critics 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, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are not guilty, asserting that the president and justice department are merely singling out them for revenge.

US District Judge Cameron Currie dismissed the indictments against them due to attorney Lindsey Halligan's invalid appointment as federal prosecutor. However, she 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 believes Trump will probably come after him again.

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

But the DOJ confronts significant obstacles to effectively try both after this defeat, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Kay Levine, law professor at Emory University.

Could the DOJ appeal?

The DOJ 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 pursue this option, pledging to use all available legal action, including an expedited appeal.

Previously, the Trump administration has strongly challenged unfavourable rulings, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to keep fighting any further politically driven indictments through all legal avenues.

In the event of an appeal, the DOJ likely would have its own attorneys argue the case, making Halligan's involvement in the appeal uncertain.

Could there be fresh indictments?

The federal prosecutors accused James Comey with lying to lawmakers and obstructing justice. Federal prosecutors charged Letitia James with bank fraud and making false statements to a financial institution.

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

Since the initial charges were dismissed (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 different attorney could bring James' case to a new grand jury and secure a fresh indictment, stated 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 strongly disputed, whether Mr Comey's case can be recharged if a properly assigned attorney is assigned and is able to secure an indictment.

He described the complex web of attorneys, courts, and motions involved as a legal quagmire with no simple answers.

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

A key issue is the statute of limitations – the deadline that prosecutors had to charge him for these specific allegations – which ended at the end of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the DOJ to refile the case.

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

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

What happens to Lindsey Halligan?

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

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

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

US attorneys are nominated by the president and require US Senate confirmation. US laws regulate how people can be appointed on a interim basis, but the judge determined that Halligan's assignment had violated these regulations.

That leaves Halligan's role on subsequent cases against both individuals, again, uncertain.

The ruling also could 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 designated her a special federal prosecutor and praised her work as outstanding.

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