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A pair of prominent opponents of former President Trump secured major legal victories on the start of the week when a US judge threw out the government's charges filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have insisted vehemently that they are not guilty, claiming that the president and justice department are merely singling out them for revenge.

US District Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's invalid assignment as federal prosecutor. However, she left the door open for the government to try again.

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Comey admitted that likelihood after the decision, stating he thinks Trump is likely to come after him again.

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

But the government faces significant hurdles to successfully prosecute either after this setback, and experts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

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

Might the DOJ challenge the ruling?

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

Attorney General Pam Bondi indicated she would pursue this option, vowing to use all available legal action, including an immediate appeal.

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

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

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

Could there be fresh indictments?

The federal prosecutors accused James Comey with lying to Congress and obstruction of justice. Federal prosecutors charged James with bank fraud and providing false information to a financial institution.

Both entered not guilty pleas. In addition to claiming Halligan was unlawfully appointed, they also asserted to be victims of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to assemble fresh grand juries and secure new indictments.

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

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

It's clear that it will be hotly contested, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is able to secure an charge.

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

It could be more difficult for the DOJ to try to bring the identical accusations against James Comey.

A key issue is the statute of limitations – the time frame that government lawyers had to indict Comey for these specific allegations – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the DOJ to refile the case.

Even so in that situation, his lawyers said it plans to argue the prosecution is out of time.

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

What is the fate of Lindsey Halligan?

In both decisions on the indictments against Comey and James, the judge was direct: Halligan was wrongly appointed.

The judge stated in the James decision that the AG's effort to appoint Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

As a result, she had no lawful authority to file the charges, the judge wrote.

US attorneys are proposed by the US president and need US Senate confirmation. US laws govern how individuals can be assigned on a temporary basis, but the judge determined that Halligan's assignment had violated these laws.

This makes Halligan's position 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 Bondi said on Monday that she designated Halligan a special US attorney and commended her work as outstanding.

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