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Two prominent critics of President Trump obtained significant legal victories on the start of the week when a US judge dismissed the federal indictments against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are merely targeting them for retaliation.

US District Judge Cameron Currie tossed the charges against them due to attorney Lindsey Halligan's invalid appointment as US attorney. But she also left the door open for the government to refile the case.

• Judge dismisses cases against former FBI chief Comey and New York AG James
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Comey acknowledged that possibility after the decision, stating he thinks Trump will probably come after him once more.

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

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

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

Could the DOJ appeal?

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 signaled she would take this route, vowing to use all available legal action, including an immediate appeal.

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

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

In the event of an appeal, the justice department probably would have its own attorneys argue the case, making Halligan's involvement in the appeal unclear.

Is it possible there be fresh indictments?

The federal prosecutors accused James Comey with lying to lawmakers and obstruction of justice. Government lawyers indicted Letitia James with financial fraud and providing false information to a financial institution.

Both entered not guilty pleas. In addition to claiming Halligan's appointment was invalid, both also asserted to be targets of retaliatory legal action.

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to assemble fresh grand juries and obtain new charges.

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

But John Day, head of the American College of Trial Lawyers, said it could be a complex process – certainly in the Comey matter.

It's clear that it will be strongly disputed, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is able to secure an charge.

He described the tangle of attorneys, courts, and motions involved as a legal quagmire with no easy solutions.

It might be harder 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 indict Comey for these specific allegations – which expired at the end of September. However, the dismissal of the charges would trigger a half-year extension for the justice department to bring the case again.

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

The decision further indicates that because the indictment is invalid, the time limit has expired and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

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

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

Therefore, she had no lawful authority to file the charges, the judge wrote.

Federal prosecutors are proposed by the president and require Senate approval. Federal statutes regulate how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had violated these regulations.

This makes Halligan's role on subsequent cases against James and Comey, once more, uncertain.

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

But Attorney General Bondi said on Monday that she designated Halligan a special federal prosecutor and commended her work as outstanding.

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