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Two high-profile opponents of former President Trump obtained significant legal victories on the start of the week when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued vehemently that they are innocent, asserting that the president and justice department are merely singling out them for revenge.

Federal Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's improper appointment as federal prosecutor. However, she left open the possibility for the federal authorities to refile the case.

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Comey acknowledged that likelihood after the decision, stating he believes Trump will probably target him once more.

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

But the DOJ confronts significant obstacles to successfully prosecute either after this defeat, and legal analysts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Might the justice department appeal?

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

US Attorney General Pam Bondi indicated she would take this route, pledging to use all available legal action, including an immediate appeal.

Previously, the former administration has strongly challenged adverse decisions, moving cases from lower courts and sometimes accelerating its petitions up to the Supreme Court.

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

If there is an appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's involvement in the appeals process uncertain.

Could there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to Congress and obstruction of justice. Government lawyers charged Letitia James with bank fraud and providing false information to a financial institution.

Each entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, they also asserted 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 different attorney could bring James' case to a different grand jury and get a fresh indictment, said Ms Levine.

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

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

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

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

A key issue is the statute of limitations – the deadline that government lawyers had to indict Comey for these particular claims – which expired 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 situation, his lawyers said it intends to contend the prosecution is past the deadline.

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

What is the fate of Lindsey Halligan?

In the pair of rulings 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 Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

Therefore, Halligan had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are nominated by the president and need US Senate confirmation. US laws regulate how people can be appointed on a interim basis, but the judge determined that Halligan's assignment had breached these laws.

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

The ruling also could raise doubts on other cases Halligan has brought in the Eastern District of Virginia where she works.

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

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