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Two prominent opponents of former President Trump achieved major legal victories on the start of the week when a US judge dismissed the federal indictments filed against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have maintained fiercely that they are innocent, asserting that the president and justice department are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's improper appointment as US attorney. But she also left open the possibility for the federal authorities to refile the case.

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

Comey admitted that possibility after the ruling, saying he believes Trump is likely to target him again.

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

But the DOJ faces significant hurdles to effectively try either after this defeat, and legal analysts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, said Kay Levine, law professor at Emory University.

Might the DOJ challenge the ruling?

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

Attorney General Pam Bondi signaled 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 fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to continue to challenge any further politically driven indictments through every lawful means available.

If there is an appeals process, the DOJ likely would have its own attorneys present the arguments, making Halligan's involvement in the appeals process unclear.

Is it possible there be fresh indictments?

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

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

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to convene new grand juries and obtain new indictments.

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

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

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

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

It might be harder for the government to try to bring the identical accusations against James Comey.

One problem is the legal time limit – the deadline that prosecutors had to charge him for these particular claims – which expired at the end of September. However, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Still in that situation, his legal team said it plans to contend the prosecution is out of time.

The decision further indicates that because the charge is invalid, the statute of limitations has expired and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the charges against Comey and James, the judge was direct: Halligan was wrongly appointed.

Judge Currie wrote in the James ruling that the Attorney General's attempt to appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

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

Federal prosecutors are nominated by the US president and require US Senate confirmation. Federal statutes regulate how individuals can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these laws.

This makes 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 works.

But Bondi said on Monday that she designated Halligan a special US attorney and praised her work as outstanding.

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