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A pair of well-known opponents of President Trump achieved significant court wins on the start of the week when a US judge threw out the government's charges against them.

For weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are simply singling out them for revenge.

US District Judge Cameron Currie tossed the indictments against them due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. However, she left the door open for the federal authorities to refile the case.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
• US judge says government 'missteps' may have tainted Comey case
• What are ex-FBI director James Comey accused of?

Comey acknowledged that possibility after the ruling, stating he believes Trump is likely to target him once more.

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

But the DOJ faces significant obstacles to effectively try both after this setback, and legal analysts hesitate to forecast what could occur next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Professor Kay Levine, Emory University School of Law professor.

Might the justice department appeal?

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

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

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

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

If there is an appeal, the DOJ probably would have its own attorneys argue the case, making Halligan's role in the appeals process unclear.

Could there be new charges?

The government accused Comey with lying to lawmakers and obstruction of justice. Government lawyers charged Letitia James with financial fraud and providing false information to a bank.

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

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

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

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

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is appointed and is can obtain an indictment.

He characterized the tangle of attorneys, courts, and motions involved as a procedural morass with no simple answers.

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

A key issue is the statute of limitations – the time frame that government lawyers had to charge him for these particular claims – which ended at the close of September. Nonetheless, the dismissal of the charges would trigger a six-month grace period for the justice department to bring the case again.

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

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

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, the judge was blunt: Halligan's appointment was improper.

Judge Currie wrote in the James ruling that the Attorney General's attempt to install Halligan as Acting US Attorney for the Virginia Eastern District was unlawful.

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

Federal prosecutors are nominated by the president and require Senate approval. US laws regulate how individuals can be assigned on a temporary basis, but the judge determined that Halligan's assignment had breached these laws.

This makes Halligan's position on future cases against James and Comey, once more, unclear.

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

But Attorney General Bondi said on Monday that she made her a special federal prosecutor and praised her work as excellent.

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