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Two well-known critics of President Trump achieved major legal victories on the start of the week when a US judge threw out the federal indictments filed against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have maintained vehemently that they are innocent, claiming that the administration and DOJ are merely targeting them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as US attorney. But she also left open the possibility for the government to refile the case.

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Comey acknowledged that likelihood after the decision, saying he thinks Trump is likely to target him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this issue.

But the government faces steep obstacles to effectively try both after this setback, and legal analysts hesitate to predict what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Kay Levine, Emory University School of Law professor.

Could the DOJ 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 signaled she would pursue this option, pledging to use all legal means, including an expedited appeal.

In other cases, the former administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically motivated charges through every lawful means available.

If there is an appeal, the DOJ likely would have its own lawyers present the arguments, making Halligan's involvement in the appeal uncertain.

Is it possible there be new charges?

The government accused Comey with making false statements to lawmakers and obstruction of justice. Government lawyers charged James with financial fraud and making false statements to a bank.

Each entered not guilty pleas. In addition to claiming Halligan's appointment was invalid, they also asserted to be targets of retaliatory legal action.

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

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

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

It's clear that it will be hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is can obtain an indictment.

He characterized the complex web of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

It could be harder for the government to try to bring the exact same charges against James Comey.

One problem is the legal time limit – the deadline that government lawyers had to indict Comey for these specific allegations – which ended at the close of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the justice department to refile the case.

Still in that case, his lawyers said it intends to contend the prosecution is out of time.

The ruling also suggests that because the charge is void, the statute of limitations has expired and there can be no further indictment, attorney Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, the judge was direct: Halligan was wrongly appointed.

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

Therefore, Halligan lacked legal power to present the indictment, the judge wrote.

Federal prosecutors are proposed by the president and require US Senate confirmation. US laws regulate how people can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these regulations.

That leaves Halligan's role on subsequent cases against James and Comey, again, uncertain.

The ruling also could cast a shadow on other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

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

The administration stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told reporters on Monday.