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A pair of high-profile opponents of President Trump achieved major legal victories on the start of the week when a US judge threw out the government's charges against them.

For weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued fiercely that they are innocent, asserting that the administration and DOJ are merely targeting them for retaliation.

US District Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the federal authorities to refile the case.

• Court throws out cases against ex-FBI director Comey and NY attorney general James
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Comey acknowledged that possibility after the ruling, saying he thinks the former president is likely to target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this issue.

But the DOJ confronts significant hurdles to effectively try either after this defeat, and experts are reluctant to forecast what could occur next due to the cases' unprecedented nature.

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

Might the DOJ challenge the ruling?

The DOJ can contest Judge Currie's ruling before a federal appeals court. In this case, that would be the Fourth Circuit Appeals Court.

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

In other cases, the Trump administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its petitions up to the US Supreme Court.

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

In the event of an appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's involvement in the appeals process uncertain.

Could there be fresh indictments?

The government charged Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted Letitia James with financial fraud and providing false information to a bank.

Both entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, they also asserted to be targets of vindictive prosecution.

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

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

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

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

He characterized the tangle of lawyers, courts, and legal filings involved as a procedural morass with no easy solutions.

It could be more difficult for the DOJ to try to bring 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 particular claims – which ended at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the DOJ to bring the case again.

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

The ruling also suggests that since the indictment is void, the time limit has expired and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

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

Judge Currie wrote in the James decision that the AG's effort to install Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

Therefore, she had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are proposed by the president and require Senate approval. US laws regulate how individuals can be assigned on a temporary basis, but the judge determined that Halligan's appointment had breached these regulations.

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

The ruling also could cast a shadow on other cases Halligan has brought in the Virginia Eastern District where she works.

But Bondi said on Monday that she made Halligan 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 the press on Monday.