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A pair of prominent critics of President Trump secured major court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are not guilty, asserting that the administration and DOJ are merely targeting them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to attorney Lindsey Halligan's improper appointment as federal prosecutor. But she also left open the possibility for the federal authorities to try again.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
• Federal judge states DOJ errors may have tainted the Comey trial
• What are ex-FBI director James Comey charged with?

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

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

But the government confronts significant obstacles to successfully prosecute both after this defeat, and legal analysts hesitate to predict what could occur next due to the cases' unprecedented nature.

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

Could the DOJ challenge the ruling?

The Department of Justice can challenge Judge Currie's ruling before a higher appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

US Attorney General Pam Bondi indicated she would take this route, vowing to use all legal means, including an immediate appeal.

Previously, the former administration has aggressively appealed adverse decisions, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

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

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

Is it possible there be fresh indictments?

The government accused James Comey with making false statements to Congress and obstruction of justice. Federal prosecutors charged James with financial fraud and providing false information to a financial institution.

Both entered not guilty pleas. In addition to arguing Halligan's appointment was invalid, both also claimed to be victims of retaliatory legal action.

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

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

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

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an charge.

He characterized the complex web of attorneys, courts, and motions involved as a procedural morass with no easy solutions.

It might be harder for the DOJ to try to file the exact same charges against James Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to charge Comey for these particular claims – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Even so in that situation, his lawyers said it intends to contend the prosecution is out of time.

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

What happens to prosecutor Lindsey Halligan?

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

The judge stated in the James decision that the AG's effort to appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was invalid.

As a result, she lacked legal power to present the indictment, she wrote.

Federal prosecutors are nominated by the US president and require Senate approval. US laws regulate how people can be appointed on a interim basis, but Judge Currie found that Halligan's assignment had breached these laws.

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

The decision might also cast a shadow on other cases Halligan has prosecuted in the Virginia Eastern District where she works.

But Attorney General Bondi said on that day that she designated her a special federal prosecutor and praised her work as outstanding.

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