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Two high-profile critics of President Trump secured major court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

For weeks since their indictments, ex-FBI chief James Comey and NY AG 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 charges in their cases due to prosecutor Lindsey Halligan's invalid appointment as federal prosecutor. But she also left the door open for the government to try again.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that likelihood after the ruling, stating he thinks the former president will probably come after him once more.

And White House spokeswoman Abigail Jackson seemed to confirm it: This isn't the final word on this issue.

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

It feels to me like unexplored legal ground, said Kay Levine, law professor at Emory University.

Could the justice department challenge the ruling?

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

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

In other cases, 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, pledged to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeal, the justice department likely would have its own attorneys present the arguments, making Halligan's role in the appeal unclear.

Is it possible there be fresh indictments?

The government accused Comey with lying to Congress and obstructing justice. Government lawyers indicted Letitia James with bank fraud and providing false information to a bank.

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, they also asserted to be victims of vindictive prosecution.

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

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

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – especially in Comey's case.

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

He described the tangle of lawyers, courts, and motions involved as a procedural morass with no easy solutions.

It could be more difficult for the government to try to bring the exact same charges against Comey.

A key issue is the legal time limit – the time frame that government lawyers had to indict him for these particular claims – which expired at the close of September. Nonetheless, the indictment's dismissal would activate a half-year extension for the DOJ to refile the case.

Still in that situation, his legal team said it intends to argue the prosecution is past the deadline.

The ruling also suggests that because the indictment is invalid, the time limit has expired and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

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

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

As a result, she lacked legal power to file the charges, she wrote.

Federal prosecutors are proposed by the US president and need US Senate confirmation. US laws regulate how people can be appointed on a temporary 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, uncertain.

The ruling also could cast a shadow on 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 praised her work as excellent.

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