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Two high-profile opponents of former President Trump obtained significant legal victories on the start of the week when a US judge threw out the federal indictments 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, asserting that the president and justice department are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's invalid assignment as federal prosecutor. But she also left the door open for the federal authorities to try again.

• Court throws out charges against former FBI chief Comey and NY attorney general James
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• What is ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the decision, stating he believes the former president will probably come after him once more.

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

But the DOJ faces significant obstacles to effectively try both after this setback, and experts hesitate to predict what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

The DOJ 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 signaled she would take this route, pledging to use all legal means, including an immediate appeal.

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

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

In the event of an appeals process, the justice department likely would have its own lawyers present the arguments, making Halligan's involvement in the appeal uncertain.

Could there be fresh indictments?

The federal prosecutors accused Comey with lying to Congress and obstructing justice. Government lawyers charged Letitia James with financial fraud and providing false information to a financial institution.

Each entered not guilty pleas. Besides claiming Halligan was unlawfully appointed, they also asserted to be targets of vindictive prosecution.

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

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

But legal expert John Day, head 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 Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an indictment.

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

It could be harder for the DOJ to try to file the exact same charges against Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to indict him for these particular claims – which ended at the end of September. However, 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 intends to argue the government is past the deadline.

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

What happens to prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

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

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

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

This makes Halligan's role on future cases against both individuals, once more, uncertain.

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

But Bondi said on Monday that she made Halligan a special federal prosecutor and praised her work as excellent.

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