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

For weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are not guilty, claiming that the administration and DOJ are merely singling out them for revenge.

Federal Judge Cameron Currie dismissed the charges in their cases due to prosecutor Lindsey Halligan's improper appointment as US attorney. But she also left the door open for the federal authorities to try again.

• Court throws out cases against former FBI chief Comey and NY attorney general James
• Federal judge states government 'missteps' may have tainted the Comey trial
• What are former FBI head James Comey charged with?

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

And White House spokesperson Abigail Jackson appeared to agree: This isn't the last chapter on this matter.

But the DOJ faces significant hurdles to effectively try either after this setback, and experts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

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

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

Previously, the former administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes fast-tracking its petitions up to the Supreme Court.

Abbe Lowell, James's lawyer, pledged to keep fighting any additional politically motivated charges through every lawful means available.

In the event of an appeals process, the justice department probably would have its own lawyers argue the case, making Halligan's involvement in the appeals process unclear.

Is it possible there be fresh indictments?

The government charged Comey with lying to lawmakers and obstruction of justice. Government lawyers indicted James with bank fraud and making false statements to a financial institution.

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

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

Based on my analysis, a new prosecutor could present James's case to a new grand jury and get a new indictment, stated Ms 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 hotly contested, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an charge.

He characterized the complex web of attorneys, courts, and legal filings involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to file the exact same charges against Comey.

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

Even so in that case, his lawyers said it intends to contend the government is past the deadline.

The decision further indicates that since the charge is void, the time limit has run and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the charges against James and Comey, Judge Currie was blunt: 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 Eastern District of Virginia was invalid.

As a result, Halligan had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are proposed by the president and require Senate approval. US laws govern how people can be appointed on a interim basis, but the judge determined that Halligan's assignment had violated these laws.

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

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

But Attorney General Bondi said on Monday that she designated her a special US attorney and praised her work as outstanding.

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