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A pair of well-known critics of former President Trump obtained significant legal victories on Monday when a US judge threw out the federal indictments filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have insisted fiercely that they are not guilty, claiming that the president and justice department are simply targeting them for retaliation.

Federal Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. But she also left the door open for the government to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• Federal judge states government 'missteps' may have compromised Comey case
• What are former FBI head James Comey accused of?

Comey admitted that likelihood after the ruling, saying he thinks the former president is likely to come after him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this matter.

But the government faces significant obstacles to successfully prosecute both after this setback, and experts are reluctant to forecast what could occur next due to the cases' unprecedented nature.

It feels to me like unexplored legal ground, said Kay Levine, law professor at Emory University.

Could the DOJ challenge the ruling?

The Department of Justice can contest the judge's decision before a federal appeals court. In this instance, 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 expedited appeal.

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

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

In the event of an appeals process, the DOJ probably would have its own lawyers present the arguments, making Halligan's role in the appeals process unclear.

Is it possible there be new charges?

The government accused James Comey with lying to lawmakers and obstructing justice. Government lawyers indicted Letitia James with bank fraud and providing false information to a financial institution.

Each pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, both also asserted to be targets of vindictive prosecution.

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

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

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

It's clear that it will be strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an charge.

He characterized the tangle of attorneys, judges, and legal filings involved as a procedural morass with no simple answers.

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

One problem is the statute of limitations – the time frame that government lawyers had to indict him for these specific allegations – which ended at the end of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to bring the case again.

Even so in that situation, his legal team said it plans to argue the prosecution is past the deadline.

The ruling also suggests that since the indictment is invalid, the statute of limitations has expired and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against James and Comey, the judge was direct: Halligan was wrongly appointed.

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

As a result, Halligan had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. Federal statutes govern how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's assignment had violated these regulations.

That leaves Halligan's role on future cases against James and Comey, again, unclear.

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

But Attorney General Bondi said on that day that she made Halligan a special US attorney and praised her work as excellent.

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.