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Two high-profile critics of President Trump achieved major legal victories on Monday when a US judge threw out the federal indictments filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, claiming that the president and justice department are simply targeting them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's improper assignment as federal prosecutor. But she also left the door open for the government to try again.

• Judge dismisses charges against ex-FBI director Comey and NY attorney general James
• US judge says government 'missteps' may have compromised the Comey trial
• What are ex-FBI director James Comey charged with?

Comey admitted that possibility after the ruling, stating he believes Trump will probably come after him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this issue.

But the DOJ confronts steep hurdles to successfully prosecute 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 uncharted territory, stated Kay Levine, law professor at Emory University.

Could the DOJ challenge the ruling?

The DOJ can contest Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

In other cases, the Trump administration has strongly challenged unfavourable rulings, moving cases from lower courts and sometimes fast-tracking its petitions up to the US Supreme Court.

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

In the event of an appeal, the justice department likely would have its own attorneys argue the case, making Halligan's role in the appeals process uncertain.

Is it possible there be fresh indictments?

The government accused Comey with making false statements to lawmakers and obstructing justice. Federal prosecutors indicted James with financial fraud and making false statements to a financial institution.

Each pleaded not guilty. Besides claiming Halligan was unlawfully appointed, both also asserted to be victims of vindictive prosecution.

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

As far as everything I've seen, a different attorney could present James's case to a new grand jury and secure 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 – especially in Comey's case.

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

He described the tangle of lawyers, judges, and legal filings involved as a procedural morass with no easy solutions.

It might be more difficult for the DOJ to try to bring the identical accusations against James Comey.

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

Still in that case, his lawyers said it intends to contend the prosecution is past the deadline.

The decision further indicates that because the charge is invalid, the time limit 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 charges against James and Comey, the judge was blunt: Halligan was wrongly appointed.

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

As a result, she lacked legal power to file the charges, the judge wrote.

Federal prosecutors are nominated by the US president and need US Senate confirmation. US laws govern how people can be appointed on a temporary basis, but the judge determined that Halligan's assignment had breached these laws.

This makes Halligan's position on future cases against James and Comey, again, unclear.

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

But Bondi said on Monday that she designated her a special US attorney and commended her work as excellent.

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