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Two high-profile opponents of President Trump obtained significant court wins on the start of the week when a US judge threw out the government's charges against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have argued vehemently that they are not guilty, claiming that the president and justice department are simply singling out them for revenge.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. However, she left open the possibility for the federal authorities to refile the case.

• Court throws out cases against ex-FBI director Comey and NY attorney general James
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• What is ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the decision, stating he believes Trump will probably come after him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the last chapter on this issue.

But the DOJ faces steep hurdles to successfully prosecute either after this defeat, and experts hesitate to forecast what could occur next due to the cases' unprecedented nature.

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

Might the DOJ appeal?

The Department of Justice can contest the judge's decision 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 available legal action, including an expedited appeal.

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

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

In the event of an appeal, the DOJ probably would have its own attorneys argue the case, making Halligan's involvement in the appeals process uncertain.

Is it possible there be fresh indictments?

The federal prosecutors accused James Comey with lying to lawmakers and obstruction of justice. Government lawyers indicted Letitia James with financial fraud and providing false information to a financial institution.

Each pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, they also claimed to be targets of retaliatory legal action.

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

Based on my analysis, a different attorney could present James's case to a new grand jury and secure a fresh indictment, said Professor Levine.

But 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 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 lawyers, judges, and motions involved as a procedural morass with no simple answers.

It might 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 prosecutors had to indict Comey for these specific allegations – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Still in that case, his legal team said it plans to contend the government is past the deadline.

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

What happens to prosecutor 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 AG's effort to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was invalid.

Therefore, she had no lawful authority to file the charges, she wrote.

US attorneys are nominated by the president and need US Senate confirmation. Federal statutes govern how individuals can be assigned on a temporary basis, but the judge determined that Halligan's assignment had breached these regulations.

This makes Halligan's role on subsequent cases against both individuals, once more, unclear.

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

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

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