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A pair of well-known critics of President Trump obtained major court wins on Monday when a US judge threw out the government's charges filed 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 not guilty, asserting that the president and justice department are simply targeting them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. However, she left open the possibility for the government to try again.

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Comey admitted that likelihood after the ruling, stating he thinks the former president will probably come after 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 steep hurdles to effectively try both after this setback, and legal analysts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Professor Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

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

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

Previously, the Trump administration has aggressively appealed adverse decisions, taking cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeals process, the DOJ likely would have its own lawyers argue the case, making Halligan's involvement in the appeals process uncertain.

Could there be new charges?

The government accused James Comey with lying to lawmakers and obstructing justice. Government lawyers charged Letitia James with bank fraud and making false statements to a bank.

Each entered not guilty pleas. Besides claiming Halligan was unlawfully appointed, they also claimed to be targets of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the government might try to assemble fresh grand juries and obtain new indictments.

Based on my analysis, a different attorney could bring James' case to a different grand jury and secure a new indictment, said Professor 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 Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

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

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

One problem is the statute of limitations – the deadline that government lawyers had to indict him for these specific allegations – which ended at the close of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to refile the case.

Still in that case, his lawyers said it plans to argue the government is past the deadline.

The decision further indicates that since the indictment is invalid, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

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

The judge stated in the James decision that the Attorney General's attempt to install Ms. Halligan as Acting US Attorney for the Virginia Eastern District was unlawful.

As a result, she lacked legal power to present the indictment, the judge wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. US laws govern how people can be assigned on a interim basis, but the judge determined that Halligan's appointment had violated these regulations.

This makes Halligan's position on future cases against both individuals, again, unclear.

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

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

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