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Two prominent critics of former President Trump obtained significant court wins on Monday when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted fiercely that they are innocent, claiming that the administration and DOJ are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the charges against them due to attorney Lindsey Halligan's invalid assignment as US attorney. However, she left open the possibility for the federal authorities to refile the case.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
• Federal judge states government 'missteps' may have compromised Comey case
• What are ex-FBI director James Comey accused of?

Comey acknowledged that possibility after the decision, stating he believes Trump is likely to target him once more.

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

But the government faces steep obstacles to effectively try both after this defeat, and legal analysts are reluctant to predict what could occur next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

The DOJ can challenge the judge's decision before a higher appeals court. In this case, that would be the Fourth Circuit Appeals Court.

Attorney General Pam Bondi indicated she would pursue this option, vowing to use all legal means, including an expedited appeal.

In other cases, the former administration has aggressively appealed unfavourable rulings, moving cases from lower courts and sometimes accelerating its requests up to the Supreme Court.

Abbe Lowell, James's lawyer, vowed to continue to challenge any further politically motivated charges through all legal avenues.

If there is an appeal, the justice department probably would have its own attorneys argue the case, making Halligan's involvement in the appeals process unclear.

Is it possible there be fresh indictments?

The federal prosecutors charged Comey with making false statements to Congress and obstructing justice. Government lawyers charged James with financial fraud and making false statements to a bank.

Each entered not guilty pleas. Besides arguing Halligan was unlawfully appointed, they also claimed to be victims of vindictive prosecution.

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

Based on my analysis, a new prosecutor 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 complex process – certainly in the Comey matter.

It's clear that it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an charge.

He described the tangle of lawyers, judges, and legal filings involved as a legal quagmire with no simple answers.

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

One problem is the legal time limit – the time frame that government lawyers had to charge Comey for these particular claims – which ended at the end of September. However, the indictment's dismissal would activate a half-year extension for the justice department to bring the case again.

Even so in that case, his legal team said it plans to contend the prosecution is out of time.

The decision further indicates that because the charge is void, the statute of limitations has expired and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

The judge stated in the James ruling that the AG's effort to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

US attorneys are proposed by the president and require US Senate confirmation. US laws regulate how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's appointment had breached these laws.

That leaves Halligan's role on subsequent cases against both individuals, again, 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 made Halligan a special federal prosecutor and praised her work as excellent.

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.