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A pair of well-known critics of President Trump secured major court wins on the start of the week when a federal judge threw out the federal indictments 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 merely targeting them for retaliation.

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

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

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

But the government confronts significant hurdles to successfully prosecute either after this setback, and legal analysts are reluctant to predict what could occur next due to the cases' unprecedented nature.

It feels to me like uncharted territory, stated Professor Kay Levine, law professor at Emory University.

Might the justice department challenge the ruling?

The Department of Justice can contest the judge's decision before a federal appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

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

Previously, the Trump administration has strongly challenged unfavourable rulings, taking cases from trial courts and sometimes accelerating its petitions up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically motivated charges through every lawful means available.

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

Is it possible there be new charges?

The government accused Comey with making false statements to Congress and obstruction of justice. Federal prosecutors indicted James with financial fraud and making false statements to a bank.

Each entered not guilty pleas. In addition to arguing Halligan's appointment was invalid, both also asserted to be targets of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the DOJ might try to assemble new grand juries and obtain new indictments.

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

But John Day, head 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 re-indicted if a properly assigned attorney is assigned and is can obtain an charge.

He described the complex web of lawyers, judges, and legal filings involved as a procedural morass with no simple answers.

It might be more difficult for the government to try to bring the exact same charges against James Comey.

A key issue is the statute of limitations – the time frame that government lawyers had to indict him 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 DOJ to bring the case again.

Still in that case, his legal team said it plans to contend the prosecution is past the deadline.

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

What happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

Judge Currie wrote in the James ruling that the Attorney General's attempt to appoint 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 require US Senate confirmation. Federal statutes regulate how people can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these laws.

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

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

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

The White House maintained its position that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.