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Two prominent opponents of President Trump obtained significant court wins on Monday when a US judge threw out the federal indictments filed against them.

For weeks following their charges, 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.

US District Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid assignment as federal prosecutor. However, she left open the possibility for the government to refile the case.

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Comey admitted that possibility after the ruling, stating he thinks Trump will probably target him once more.

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

But the DOJ faces significant hurdles to effectively try either after this defeat, and experts hesitate to predict what could occur next due to the cases' unprecedented nature.

It feels to me like 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 federal appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

US 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 aggressively appealed unfavourable rulings, taking cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to keep fighting any additional politically motivated charges through every lawful means available.

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

Is it possible there be fresh indictments?

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

Both entered not guilty pleas. In addition to claiming Halligan was unlawfully appointed, they also claimed to be victims of vindictive prosecution.

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

As far as everything I've seen, a new prosecutor could present James's case to a new grand jury and secure a new indictment, said Ms Levine.

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

It's clear that it will be strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an indictment.

He described the complex web of lawyers, judges, and legal filings involved as a procedural morass with no simple answers.

It could be more difficult for the government to try to file the identical accusations against Comey.

A key issue is the statute of limitations – the deadline that prosecutors had to charge Comey for these particular claims – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a half-year extension for the DOJ to bring the case again.

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

The ruling also suggests that because the indictment is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, the judge was direct: Halligan was wrongly appointed.

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 unlawful.

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

Federal prosecutors are nominated by the president and require US Senate confirmation. US laws regulate how individuals can be assigned on a interim basis, but Judge Currie found that Halligan's appointment had breached these regulations.

This makes Halligan's role on subsequent cases against James and Comey, again, uncertain.

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

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

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