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Two high-profile opponents of President Trump achieved significant court wins on Monday when a federal 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 not guilty, asserting that the administration and DOJ are merely singling out them for revenge.

US District Judge Cameron Currie tossed the indictments in their cases due to attorney Lindsey Halligan's improper appointment as US attorney. However, she left the door open for the government to refile the case.

• Court throws out charges against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have tainted Comey case
• What is former FBI head James Comey charged with?

Comey acknowledged that possibility after the ruling, saying he believes the former president is likely to target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the last chapter on this issue.

But the DOJ faces significant obstacles to successfully prosecute either after this setback, and experts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Kay Levine, law professor at Emory University.

Might the justice department appeal?

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

Attorney General Pam Bondi signaled she would pursue this option, pledging to use all available legal action, including an expedited appeal.

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

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

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

Could there be new charges?

The government accused James Comey with lying to Congress and obstruction of justice. Federal prosecutors indicted Letitia James with financial fraud and making false statements to a financial institution.

Both pleaded not guilty. Besides arguing Halligan's appointment was invalid, they also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to assemble fresh grand juries and secure new indictments.

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

It's clear that it will be strongly disputed, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an charge.

He described the tangle of attorneys, courts, and legal filings involved as a legal quagmire with no simple answers.

It could be harder for the government to try to bring the identical accusations against Comey.

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

Still in that situation, his legal team said it plans to argue the prosecution is out of time.

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

What happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was direct: Halligan's appointment was improper.

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

As a result, Halligan had no lawful authority to file the charges, the judge wrote.

US attorneys are nominated by the US president and need US Senate confirmation. US laws govern how individuals can be appointed on a interim basis, but the judge determined that Halligan's appointment had violated these regulations.

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

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 Monday that she designated Halligan a special US attorney 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.