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Two prominent opponents of President Trump secured significant court wins on Monday when a federal judge threw out the government's charges against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have maintained fiercely that they are innocent, claiming that the president and justice department are merely targeting them for revenge.

Federal Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's improper appointment as US attorney. But she also left the door open for the government to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
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Comey admitted that possibility after the decision, saying he believes Trump is likely to target him again.

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

But the government confronts significant obstacles to successfully prosecute either after this defeat, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

The DOJ can challenge Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

Attorney General Pam Bondi indicated she would pursue this option, vowing to use all legal means, including an expedited appeal.

In other cases, the Trump administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its petitions up to the Supreme Court.

Abbe Lowell, an attorney representing James, vowed to continue to challenge any further politically driven indictments through every lawful means available.

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

Could there be new charges?

The government accused James Comey with making false statements to Congress and obstructing justice. Federal prosecutors indicted Letitia James with financial fraud and providing false information to a bank.

Both pleaded not guilty. Besides arguing Halligan's appointment was invalid, they also claimed to be victims of retaliatory legal action.

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

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

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – especially in the Comey matter.

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

He described the complex web of attorneys, courts, and legal filings involved as a procedural morass with no easy solutions.

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 government lawyers had to charge Comey for these specific allegations – which expired at the close of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the DOJ to bring the case again.

Even so in that case, his legal team said it intends to contend the prosecution is past the deadline.

The ruling also suggests that since the indictment is invalid, the statute of limitations has expired and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of prosecutor Lindsey Halligan?

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

Judge Currie wrote in the James decision that the AG's effort to install Ms. Halligan as Interim US Attorney for the Eastern District of Virginia was invalid.

Therefore, Halligan lacked legal power to file the charges, the judge wrote.

Federal prosecutors are proposed by the US president and require US Senate confirmation. US laws regulate how individuals 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 subsequent cases against both individuals, again, unclear.

The decision might also 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 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.