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Two prominent critics of President Trump achieved significant court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the administration and DOJ are simply targeting them for revenge.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. But she also left the door open for the government to try again.

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Comey admitted that likelihood after the ruling, stating he thinks the former president will probably come after him again.

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

But the government faces significant obstacles to successfully prosecute both after this setback, and legal analysts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, stated Kay Levine, law professor at Emory University.

Could the justice department appeal?

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

Attorney General Pam Bondi signaled she would take this route, vowing to use all available legal action, including an expedited appeal.

Previously, the Trump administration has aggressively appealed adverse decisions, taking cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to keep fighting any additional politically motivated charges through every lawful means available.

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

Is it possible there be fresh indictments?

The federal prosecutors accused James Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted Letitia James with bank fraud and making false statements to a financial institution.

Each entered not guilty pleas. In addition to arguing Halligan's appointment was invalid, they also asserted to be targets of vindictive prosecution.

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

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

But John Day, president 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 hotly contested, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

He characterized the tangle of lawyers, judges, and legal filings involved as a procedural morass with no simple answers.

It might be more difficult for the DOJ to try to file the identical accusations against James Comey.

A key issue is the legal time limit – the deadline that government lawyers had to charge Comey for these particular claims – which ended at the end of September. However, the indictment's dismissal would activate a half-year extension for the DOJ to bring the case again.

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

The decision further indicates that because the indictment is invalid, the time limit has run and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

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

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

US attorneys are proposed by the US president and need US Senate confirmation. US laws regulate how people can be appointed on a interim basis, but Judge Currie found that Halligan's appointment had violated these laws.

That leaves Halligan's position on future cases against James and Comey, once more, uncertain.

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

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

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.