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Two prominent opponents of former President Trump obtained significant court wins on the start of the week when a federal judge threw out the federal indictments against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, 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 prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. But she also left open the possibility for the government to try again.

• Judge dismisses cases against ex-FBI director Comey and New York AG James
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Comey admitted that possibility after the decision, saying he believes Trump will probably come after him once more.

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

But the DOJ faces significant obstacles to successfully prosecute either after this defeat, and legal analysts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Professor Kay Levine, law professor at Emory University.

Might the DOJ appeal?

The DOJ can contest Judge Currie's ruling before a higher appeals court. In this instance, 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 expedited appeal.

Previously, the former administration has strongly challenged unfavourable rulings, moving cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

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

In the event of an appeal, the DOJ probably would have its own lawyers present the arguments, making Halligan's role in the appeals process uncertain.

Is it possible there be new charges?

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

Each pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, they also asserted to be victims of vindictive prosecution.

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

Based on my analysis, a different attorney could present James's case to a new grand jury and secure a fresh indictment, stated Ms Levine.

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

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is able to secure an charge.

He described the tangle of attorneys, judges, and legal filings involved as a procedural morass with no easy solutions.

It might be harder for the government to try to bring the identical accusations against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to charge Comey for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would activate a half-year extension for the justice department to bring the case again.

Even so in that situation, his legal team said it intends to contend the government is past the deadline.

The decision further indicates that since the charge 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 both decisions on the charges against James and Comey, the judge was direct: Halligan's appointment was improper.

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

Therefore, she had no lawful authority 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 Judge Currie found that Halligan's assignment had breached these regulations.

That leaves Halligan's role on future cases against James and Comey, again, unclear.

The ruling also could raise doubts on other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

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

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