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

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained fiercely that they are innocent, claiming that the administration and DOJ are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's improper appointment as US attorney. 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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• What are former FBI head James Comey charged with?

Comey acknowledged that likelihood after the ruling, saying he believes Trump will probably target him again.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the last chapter on this issue.

But the government faces significant obstacles to successfully prosecute both after this setback, and legal analysts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Professor Kay Levine, law professor at Emory University.

Might the justice department 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 pursue this option, pledging to use all available legal action, including an expedited appeal.

Previously, the Trump administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any further politically driven indictments through all legal avenues.

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

Could there be new charges?

The government accused Comey with making false statements to lawmakers and obstruction of justice. Government lawyers indicted 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, both also claimed to be targets of retaliatory legal action.

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

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

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complicated path – especially in the Comey matter.

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

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

It could be harder for the government to try to bring the exact same charges against Comey.

A key issue is the statute of limitations – the deadline that prosecutors had to charge Comey for these particular claims – which expired at the end of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the justice department to refile the case.

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

The ruling also suggests that because the charge is void, 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 blunt: Halligan's appointment was improper.

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

Therefore, she lacked legal power to present the indictment, she wrote.

US attorneys are nominated by the president and need Senate approval. US laws govern how individuals can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

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

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 that day that she designated her a special federal prosecutor and praised her work as excellent.

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