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A pair of well-known opponents of President Trump achieved major court wins on the start of the week when a federal judge dismissed the federal indictments against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have argued vehemently that they are not guilty, claiming that the president and justice department are merely targeting them for retaliation.

US District Judge Cameron Currie dismissed the indictments in their cases due to attorney Lindsey Halligan's improper assignment as federal prosecutor. However, she left open the possibility for the federal authorities to try again.

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Comey acknowledged that likelihood after the ruling, saying he thinks Trump is likely to target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This will not be the last chapter on this issue.

But the government confronts significant hurdles to effectively try both after this defeat, and experts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Kay Levine, law professor at Emory University.

Could the justice department appeal?

The DOJ can challenge Judge Currie's ruling before a higher appeals court. In this case, 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 expedited appeal.

Previously, the Trump administration has strongly challenged unfavourable rulings, moving cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

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

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

Could there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstruction of justice. Federal prosecutors indicted Letitia James with financial fraud and providing false information to a financial institution.

Both entered not guilty pleas. In addition to claiming Halligan's appointment was invalid, both also claimed to be victims of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the government might try to assemble new grand juries and obtain new charges.

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

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

It's clear that it will be strongly disputed, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is able to secure an charge.

He described the complex web of attorneys, courts, and legal filings involved as a legal quagmire with no simple answers.

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

One problem is the statute of limitations – the deadline that prosecutors had to charge him for these particular claims – which ended at the end of September. However, the indictment's dismissal would activate a six-month grace period for the DOJ to bring the case again.

Still in that case, his legal team said it intends to argue the prosecution is out of time.

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

What happens to Lindsey Halligan?

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

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

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

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

That leaves Halligan's role on future cases against both individuals, once more, unclear.

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

But Attorney General Bondi said on Monday that she made Halligan a special US attorney and praised her work as outstanding.

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