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A pair of prominent opponents of President Trump secured major court wins on the start of the week when a US judge threw out the government's charges filed against them.

For weeks following their charges, former FBI Director James Comey and NY AG Letitia James have argued fiercely that they are not guilty, claiming that the president and justice department are merely targeting them for retaliation.

Federal Judge Cameron Currie tossed the indictments against them due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. However, she left the door open for the government to try again.

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

And White House spokeswoman Abigail Jackson appeared to agree: This isn't the final word on this matter.

But the government confronts significant hurdles to successfully prosecute either after this setback, and legal analysts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

The DOJ can contest the judge's decision before a higher appeals court. In this case, that would be the Fourth Circuit Appeals Court.

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

In other cases, the Trump administration has strongly challenged adverse decisions, moving cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

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

In the event of an appeal, the DOJ probably would have its own lawyers argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be new charges?

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

Each pleaded not guilty. In addition to arguing Halligan's appointment was invalid, both also claimed to be victims of retaliatory legal action.

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

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and get a fresh indictment, stated Ms Levine.

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – 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 tangle of attorneys, courts, and motions involved as a legal quagmire with no simple answers.

It might be harder for the DOJ to try to file the exact same charges against James Comey.

A key issue is the legal time limit – the time frame that prosecutors had to charge him for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a six-month grace period for the justice department to refile the case.

Still in that case, his legal team said it plans to contend the government is out of time.

The decision further indicates that since the indictment is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

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

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

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

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

That leaves Halligan's position on subsequent cases against both individuals, again, uncertain.

The decision might also raise doubts on any other cases Halligan has brought in the Virginia Eastern District where she works.

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

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