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A pair of high-profile critics of President Trump achieved major court wins on Monday when a federal judge threw out the federal indictments against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, asserting that the president and justice department are merely singling out them for retaliation.

Federal Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. However, she left open the possibility for the government to try again.

• Court throws out charges against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have tainted the Comey trial
• What are ex-FBI director James Comey accused of?

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

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the final word on this matter.

But the DOJ faces steep obstacles to effectively try both after this defeat, and experts 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.

Could the DOJ challenge the ruling?

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

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

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

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

If there is an appeal, the DOJ probably would have its own lawyers present the arguments, making Halligan's role in the appeals process uncertain.

Is it possible there be new charges?

The government accused Comey with making false statements to lawmakers and obstruction of justice. Government lawyers charged Letitia James with bank fraud and providing false information to a bank.

Each entered not guilty pleas. Besides arguing Halligan's appointment was invalid, both also claimed to be targets of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to assemble fresh 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, said Ms Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – 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 indictment.

He characterized the tangle of attorneys, judges, and motions involved as a legal quagmire with no simple answers.

It might be more difficult for the DOJ to try to file the exact same charges against Comey.

One problem is the statute of limitations – the deadline that prosecutors had to charge 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 case, his lawyers said it intends to argue the government is out of time.

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

What happens to Lindsey Halligan?

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

Judge Currie wrote 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, Halligan lacked legal power to file the charges, she wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. Federal statutes regulate how individuals can be appointed on a interim basis, but the judge determined that Halligan's appointment had breached these laws.

This makes Halligan's role on subsequent cases against both individuals, again, uncertain.

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

But Bondi said on that day that she made her a special US attorney and commended her work as outstanding.

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