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Two high-profile opponents of President Trump achieved significant court wins on the start of the week when a US judge threw out the federal indictments against them.

For weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have argued fiercely that they are innocent, asserting that the president and justice department are merely targeting them for revenge.

US District Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. But she also left open the possibility for the federal authorities to refile the case.

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Comey acknowledged that possibility after the decision, saying he believes the former president will probably come after him again.

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

But the government confronts steep hurdles to effectively try both after this setback, and experts hesitate to forecast what could happen next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, stated Kay Levine, law professor at Emory University.

Could the justice department challenge the ruling?

The DOJ can challenge Judge Currie's ruling before a higher appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

Previously, the Trump administration has aggressively appealed unfavourable rulings, moving cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to continue to challenge any additional politically driven indictments through every lawful means available.

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

Could there be new charges?

The government charged Comey with making false statements to Congress and obstructing justice. Government lawyers indicted Letitia James with bank fraud and making false statements to a financial institution.

Both 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 (although appeals might alter this), the DOJ might try to convene new grand juries and secure new charges.

Based on my analysis, a different attorney could bring James' 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 complex process – certainly in the Comey matter.

I can tell you it will be strongly disputed, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is able to secure an charge.

He characterized the complex web of lawyers, courts, and legal filings involved as a procedural morass with no simple answers.

It could be harder for the DOJ to try to bring the identical accusations against Comey.

One problem is the legal time limit – the deadline that government lawyers had to indict Comey for these particular claims – which expired at the end of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the DOJ to refile the case.

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

The decision further indicates that because the charge is void, the time limit has expired and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

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

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

Therefore, she had no lawful authority to file the charges, she wrote.

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

That leaves Halligan's position on subsequent cases against James and Comey, again, unclear.

The ruling also could raise doubts on any other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

But Bondi said on Monday that she designated Halligan a special US attorney and commended her work as excellent.

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