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

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, asserting that the administration and DOJ are merely singling out them for retaliation.

US District Judge Cameron Currie dismissed the indictments 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 try again.

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Comey admitted that likelihood after the ruling, stating he thinks the former president is likely to come after him again.

And White House spokesperson Abigail Jackson appeared to agree: This will not be the final word on this matter.

But the DOJ confronts significant obstacles to effectively try either after this setback, and legal analysts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Kay Levine, law professor at Emory University.

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 pursue this option, vowing to use all legal means, including an immediate appeal.

In other cases, the former administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to keep fighting any additional politically driven indictments 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 appeals process uncertain.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstructing justice. Government lawyers charged James with bank fraud and providing false information to a bank.

Both pleaded not guilty. Besides arguing Halligan's appointment was invalid, both also claimed to be targets of vindictive prosecution.

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

Based on my analysis, a new prosecutor could present James's case to a different grand jury and secure a new indictment, stated Professor Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly 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 assigned and is can obtain an indictment.

He described the complex web of attorneys, courts, and legal filings involved as a procedural morass with no easy solutions.

It could be more difficult for the government to try to file the identical accusations against James Comey.

A key issue is the legal time limit – the time frame that government lawyers had to charge him for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a six-month grace period for the DOJ to refile the case.

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

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

What is the fate of Lindsey Halligan?

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

Judge Currie wrote in the James ruling that the AG's effort to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

As a result, she lacked legal power to file the charges, she wrote.

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

This makes Halligan's position on subsequent cases against James and Comey, once more, uncertain.

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

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

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