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Two well-known opponents of President Trump achieved major court wins on Monday when a US judge threw out the government's charges filed against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained fiercely that they are not guilty, asserting that the president and justice department are merely singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's invalid assignment as federal prosecutor. But she also left the door open for the federal authorities to refile the case.

• Judge dismisses cases against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have compromised Comey case
• What is former FBI head James Comey charged with?

Comey acknowledged that likelihood after the ruling, stating he thinks the former president is likely to 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 faces steep obstacles to effectively try either after this defeat, and legal analysts are reluctant to forecast what could occur next due to the cases' unprecedented nature.

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

Could the DOJ challenge the ruling?

The Department of Justice can contest 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, pledging to use all legal means, including an expedited appeal.

In other cases, the former administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically driven indictments through every lawful means available.

If there is an appeals process, the DOJ probably would have its own lawyers argue the case, making Halligan's involvement in the appeals process uncertain.

Could there be new charges?

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

Both entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, both also claimed to be targets of retaliatory legal action.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to convene new grand juries and obtain new charges.

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

But John Day, head of the American College of Trial Lawyers, said it could be a complex process – especially in the Comey matter.

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

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

It could be more difficult for the DOJ to try to file the identical accusations against James Comey.

One problem is the legal time limit – the time frame that government lawyers had to charge him for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the justice department to refile the case.

Even so in that situation, his lawyers said it intends to contend the prosecution is past the deadline.

The ruling also suggests that since the indictment is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

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

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

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

US attorneys are nominated by the US president and require US Senate confirmation. US laws govern how people can be assigned on a interim basis, but Judge Currie found that Halligan's appointment had breached these laws.

This makes Halligan's role on future cases against James and Comey, once more, unclear.

The decision might also raise doubts on any other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

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

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