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

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

US District Judge Cameron Currie dismissed the charges against them due to attorney Lindsey Halligan's improper appointment as US attorney. However, she left the door open for the federal authorities to try again.

• Judge dismisses cases against ex-FBI director Comey and New York AG James
• Federal judge states government 'missteps' may have tainted the Comey trial
• What is ex-FBI director James Comey charged with?

Comey acknowledged that likelihood after the decision, saying he believes the former president will probably target him again.

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

But the DOJ confronts steep obstacles to effectively try either after this defeat, 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.

Might the justice department appeal?

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

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

Previously, the former administration has aggressively appealed adverse decisions, moving cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically driven indictments through all legal avenues.

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

Could there be fresh indictments?

The federal prosecutors charged Comey with making false statements to lawmakers and obstruction of justice. Federal prosecutors charged Letitia James with bank fraud and providing false information to a financial institution.

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, both also asserted to be victims of retaliatory legal action.

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

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

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

It's clear that it will be hotly contested, whether Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an indictment.

He described the complex web of lawyers, courts, and motions involved as a legal quagmire with no easy solutions.

It could be harder for the DOJ to try to file the exact same charges against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to charge Comey for these specific allegations – which ended at the close of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the DOJ to refile the case.

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

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

What happens to Lindsey Halligan?

In both decisions on the charges against James and Comey, Judge Currie was direct: Halligan's appointment was improper.

Judge Currie wrote in the James decision that the Attorney General's attempt to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

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

Federal prosecutors are proposed by the president and need US Senate confirmation. Federal statutes govern how individuals can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

That leaves Halligan's role on subsequent cases against both individuals, again, unclear.

The decision might also cast a shadow on other cases Halligan has brought in the Eastern District of Virginia where she works.

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

The administration stood by its stance that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.