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Two well-known critics of former President Trump secured major court wins on the start of the week when a US judge threw out the government's charges against them.

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted vehemently that they are innocent, claiming that the president and justice department are simply 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 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 once more.

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

But the DOJ confronts significant obstacles to successfully prosecute either after this setback, and legal analysts hesitate to forecast what could occur next due to the cases' unprecedented nature.

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

Might the DOJ 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 Appeals Court.

Attorney General Pam Bondi indicated she would take this route, pledging to use all legal means, including an expedited appeal.

Previously, the Trump administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically driven indictments through every lawful means available.

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

Is it possible there be fresh indictments?

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

Both pleaded not guilty. Besides arguing Halligan's appointment was invalid, both also asserted to be targets of retaliatory legal action.

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

As far as everything I've seen, a different attorney could present James's case to a different grand jury and get a fresh indictment, said Ms Levine.

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

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

He characterized the complex web of attorneys, courts, and motions involved as a legal quagmire with no simple answers.

It might be harder for the DOJ to try to file the identical accusations against James Comey.

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

Even so in that situation, his legal team said it intends to argue the prosecution is past the deadline.

The ruling also suggests that since the charge is invalid, the time limit has expired and there can be no further indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, the judge was blunt: 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 Eastern District of Virginia was unlawful.

Therefore, Halligan lacked legal power to present the indictment, the judge wrote.

US attorneys are proposed by the president and require US Senate confirmation. Federal statutes govern how individuals can be assigned on a temporary basis, but Judge Currie found that Halligan's appointment had breached these laws.

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

The ruling also could raise doubts on other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

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

The administration maintained its position that Halligan's appointment was legal, press secretary Karoline Leavitt told the press on Monday.