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

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have argued fiercely that they are innocent, claiming that the president and justice department are simply singling out them for retaliation.

Federal Judge Cameron Currie dismissed the indictments against them due to attorney Lindsey Halligan's invalid appointment as US attorney. However, she left open the possibility for the government to try again.

• Court throws out charges against ex-FBI director Comey and New York AG James
• US judge says government 'missteps' may have tainted the Comey trial
• What are former FBI head James Comey charged with?

Comey admitted that likelihood after the decision, stating he believes Trump will probably come after him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this issue.

But the government faces significant hurdles to successfully prosecute either after this defeat, and legal analysts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, stated Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

The DOJ can contest the judge's decision before a higher appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

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

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

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any further politically driven indictments through all legal avenues.

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

Is it possible there be fresh indictments?

The federal prosecutors accused James Comey with making false statements to Congress and obstruction of justice. Federal prosecutors charged Letitia James with bank fraud and providing false information to a bank.

Both pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, both also asserted 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 secure new indictments.

As far as everything I've seen, a new prosecutor could bring James' case to a new grand jury and get a new indictment, said Professor Levine.

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

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

He characterized the tangle of attorneys, courts, and motions involved as a legal quagmire with no simple answers.

It might be harder 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 charge him for these particular claims – which ended at the end of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to refile the case.

Even so in that case, his lawyers said it intends to argue the government is out of time.

The ruling also suggests that because the charge is void, the statute of limitations 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 indictments against Comey and James, Judge Currie was blunt: Halligan's appointment was improper.

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

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

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

That leaves Halligan's role on future cases against both individuals, again, unclear.

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

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

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