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Two well-known opponents of former President Trump secured significant court wins on the start of the week when a federal judge threw out the government's charges against them.

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued vehemently that they are not guilty, asserting that the president and justice department are merely singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. However, she left the door open for the government to refile the case.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
• Federal judge states government 'missteps' may have tainted Comey case
• What is ex-FBI director James Comey accused of?

Comey admitted that likelihood after the decision, saying he thinks the former president is likely to come after him once more.

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

But the DOJ confronts steep obstacles to successfully prosecute both after this setback, and legal analysts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Professor 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 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 unfavourable rulings, taking cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any further politically motivated charges through every lawful means available.

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

Could there be new charges?

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

Each pleaded not guilty. In addition to claiming Halligan's appointment was invalid, both also claimed to be targets of retaliatory legal action.

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

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

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – especially in the Comey matter.

I can tell you it will be hotly contested, whether Mr Comey's case can be recharged if a lawfully appointed prosecutor is assigned and is able to secure an charge.

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

It could be more difficult for the government to try to file the exact same charges against James Comey.

One problem is the statute of limitations – the deadline that prosecutors had to charge Comey for these particular claims – which expired at the close of September. However, the dismissal of the charges would activate a half-year extension for the justice department to bring the case again.

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

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

What is the fate of Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, the judge was blunt: Halligan was wrongly appointed.

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

As a result, Halligan had no lawful authority to file the charges, she wrote.

Federal prosecutors are nominated by the US president and need Senate approval. US laws govern how people can be assigned on a temporary basis, but Judge Currie found that Halligan's assignment had breached these laws.

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

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

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

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.