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Two prominent opponents of former President Trump obtained major legal victories on the start of the week when a US judge threw out the government's charges against them.

For weeks following their charges, former FBI Director James Comey and NY AG Letitia James have insisted fiercely that they are innocent, claiming that the administration and DOJ are simply singling out them for retaliation.

Federal Judge Cameron Currie dismissed the indictments in their cases due to attorney Lindsey Halligan's improper assignment as US attorney. But she also left the door open for the government to try again.

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

Comey admitted that likelihood after the ruling, saying he thinks the former president will probably target him once more.

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

But the government faces significant hurdles to successfully prosecute both after this setback, and experts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, stated Kay Levine, Emory University School of Law professor.

Might the justice department challenge the ruling?

The Department of Justice 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 signaled she would pursue this option, pledging to use all legal means, including an expedited appeal.

In other cases, the Trump administration has strongly challenged unfavourable rulings, taking cases from trial courts and sometimes accelerating its petitions up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeal, the DOJ probably would have its own attorneys present the arguments, making Halligan's role in the appeals process uncertain.

Could there be new charges?

The federal prosecutors charged James Comey with making false statements to Congress and obstructing justice. Government lawyers charged James with bank fraud and making false statements to a financial institution.

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

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to assemble fresh grand juries and secure new indictments.

Based on my analysis, a different attorney could present James's case to a different grand jury and secure a fresh indictment, said Professor Levine.

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

I can tell you it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an indictment.

He described the tangle of attorneys, courts, and motions involved as a legal quagmire with no easy solutions.

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

One problem is the statute of limitations – the deadline that prosecutors had to indict him for these specific allegations – which expired at the close of September. Nonetheless, the indictment's dismissal would trigger 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 past the deadline.

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

What is the fate of Lindsey Halligan?

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

The judge stated in the James decision that the Attorney General's attempt to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

Federal prosecutors are nominated by the president and require US Senate confirmation. Federal statutes regulate how individuals can be appointed on a interim basis, but Judge Currie found that Halligan's appointment had breached these regulations.

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

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

But Bondi said on that day that she made Halligan a special US attorney and praised her work as outstanding.

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