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Two prominent opponents of former President Trump obtained major court wins on the start of the week when a federal judge threw out the federal indictments against them.

For weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, claiming that the administration and DOJ are simply targeting them for revenge.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. But she also left the door open for the federal authorities to refile the case.

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Comey acknowledged that likelihood after the ruling, stating he thinks Trump 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 issue.

But the government confronts significant hurdles to effectively try both after this setback, and legal analysts hesitate to forecast what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Professor Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

The Department of Justice can contest Judge Currie's ruling 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 immediate appeal.

Previously, the Trump administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

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

If there is an appeals process, the DOJ likely would have its own attorneys present the arguments, making Halligan's involvement in the appeal unclear.

Could there be fresh indictments?

The government charged Comey with making false statements to Congress and obstruction of justice. Federal prosecutors charged 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 claimed to be targets of vindictive prosecution.

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

As far as everything I've seen, a new prosecutor could bring James' case to a different grand jury and get a new indictment, stated Ms Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in Comey's case.

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

He characterized the tangle of lawyers, courts, and legal filings involved as a procedural morass with no easy solutions.

It might be more difficult for the DOJ to try to bring the exact same charges against James Comey.

A key issue is the legal time limit – the deadline that prosecutors had to charge Comey for these particular claims – which ended at the end of September. However, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Still in that case, his lawyers said it intends to contend the prosecution is out of time.

The decision further indicates that since the indictment is void, the statute of limitations has expired and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In both decisions on the indictments 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 install Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

Therefore, Halligan had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are proposed by the president and need US Senate confirmation. US laws regulate how individuals can be appointed on a temporary basis, but the judge determined that Halligan's appointment had breached these laws.

That leaves Halligan's position on future cases against James and Comey, once more, unclear.

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

But Bondi said on that day that she designated Halligan a special US attorney and praised her work as excellent.

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