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Two high-profile opponents of President Trump achieved major legal victories on Monday when a federal judge threw out the government's charges filed against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, claiming that the administration and DOJ are simply targeting them for retaliation.

US District Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid appointment as federal prosecutor. But she also left open the possibility for the federal authorities to try again.

• Judge dismisses charges against former FBI chief Comey and New York AG James
• Federal judge states DOJ errors may have compromised the Comey trial
• What are ex-FBI director James Comey accused of?

Comey acknowledged that possibility after the decision, saying he thinks Trump is likely to come after him once more.

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

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

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

Might the DOJ 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 Court of Appeals.

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

Previously, the Trump administration has aggressively appealed adverse decisions, moving cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge 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 attorneys argue the case, making Halligan's involvement in the appeal uncertain.

Could there be new charges?

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

Both pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, both also asserted to be targets of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the government might try to assemble fresh grand juries and obtain new indictments.

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and secure a fresh indictment, stated Ms Levine.

But legal expert 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 Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an indictment.

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

It might be harder for the government to try to bring the exact same charges against James Comey.

One problem is the legal time limit – the deadline that government lawyers had to charge Comey for these particular claims – which expired at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the justice department 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 since 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 indictments against James and Comey, Judge Currie was direct: Halligan was wrongly appointed.

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

As a result, Halligan had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are nominated by the president and need Senate approval. Federal statutes govern how individuals can be appointed on a interim basis, but the judge determined that Halligan's appointment had violated these regulations.

This makes Halligan's role on future cases against James and Comey, once more, unclear.

The decision might also cast a shadow on other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

But Attorney General Bondi said on Monday that she made her a special federal prosecutor and commended her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told reporters on Monday.