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

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have maintained vehemently that they are innocent, claiming that the administration and DOJ are simply singling out them for revenge.

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

• Judge dismisses cases against former FBI chief Comey and NY attorney general James
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Comey admitted that likelihood after the ruling, saying he thinks Trump is likely to target him once more.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the government faces steep hurdles to successfully prosecute both after this setback, and legal analysts are reluctant 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 DOJ appeal?

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

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

In other cases, the former administration has aggressively appealed adverse decisions, taking cases from lower courts and sometimes fast-tracking its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to keep fighting any further politically motivated charges through all legal avenues.

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

Could there be new charges?

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

Both pleaded not guilty. Besides arguing Halligan was unlawfully appointed, they also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (though, of course, appeals could change that), the government might try to convene new grand juries and obtain new indictments.

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

But legal expert 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 Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is can obtain an charge.

He described the tangle of attorneys, courts, and motions involved as a legal quagmire with no easy solutions.

It might be more difficult for the DOJ to try to bring the exact same charges against Comey.

A key issue is the statute of limitations – the time frame that government lawyers had to charge Comey for these particular claims – which ended at the end of September. Nonetheless, the indictment's dismissal would activate 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 argue the prosecution is out of time.

The decision further indicates that because the charge is void, the time limit has run and there can be no new indictment, attorney 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 was wrongly appointed.

The judge stated in the James decision that the Attorney General's attempt to install Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

Therefore, she lacked legal power to present the indictment, she wrote.

US attorneys are proposed by the US president and require US Senate confirmation. Federal statutes govern how people can be assigned on a temporary 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, unclear.

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

But Bondi said on Monday that she made her a special US attorney and praised her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told reporters on Monday.