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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 federal indictments filed against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have insisted 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 indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. But she also left the door open for the federal authorities to refile the case.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that likelihood after the decision, saying he thinks the former president will probably target him again.

And White House spokeswoman Abigail Jackson seemed to confirm it: This will not be the last chapter on this matter.

But the government confronts significant obstacles to successfully prosecute either after this setback, and experts hesitate to forecast 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.

Could the DOJ challenge the ruling?

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

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

In other cases, the Trump administration has aggressively appealed unfavourable rulings, taking cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Abbe Lowell, James's lawyer, vowed to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeals process, the DOJ probably would have its own lawyers present the arguments, making Halligan's role in the appeal uncertain.

Could there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to Congress and obstructing justice. Government lawyers indicted James with bank fraud and making false statements to a bank.

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

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

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

But legal expert 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 strongly disputed, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an indictment.

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

It could be more difficult for the DOJ to try to bring the identical accusations against James Comey.

One problem is the legal time limit – the deadline that prosecutors had to indict Comey for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to refile the case.

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

The ruling also suggests that because the charge is void, the time limit has expired and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

Judge Currie wrote in the James ruling that the AG's effort to install Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

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

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

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

The decision might also cast a shadow on any other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

But Bondi said on that day that she made her a special US attorney and commended her work as outstanding.

The administration maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.