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A pair of well-known critics of President Trump achieved significant court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently that they are not guilty, claiming that the president and justice department are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as US attorney. However, she left the door open for the federal authorities to refile the case.

• Judge dismisses cases against former FBI chief Comey and New York AG James
• Federal judge states DOJ errors may have tainted Comey case
• What are ex-FBI director James Comey charged with?

Comey acknowledged that likelihood after the decision, stating he thinks Trump is likely to target him again.

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

But the government faces significant obstacles to successfully prosecute either after this defeat, and legal analysts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Kay Levine, law professor at Emory University.

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 Appeals Court.

US Attorney General Pam Bondi indicated she would pursue this option, vowing to use all legal means, including an immediate appeal.

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

Abbe Lowell, an attorney representing James, vowed to keep fighting any further politically driven indictments through every lawful means available.

In the event of an appeals process, the DOJ likely would have its own lawyers present the arguments, making Halligan's role in the appeal unclear.

Could there be fresh indictments?

The government charged Comey with making false statements to Congress and obstructing justice. Government lawyers charged James with bank fraud and making false statements to a bank.

Both pleaded not guilty. Besides arguing Halligan was unlawfully appointed, both also asserted to be victims of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to convene new grand juries and obtain 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 fresh indictment, stated Ms Levine.

But John Day, president 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 strongly disputed, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an charge.

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

It might be more difficult for the DOJ to try to bring the identical accusations against Comey.

A key issue is the legal time limit – the time frame that government lawyers had to charge Comey for these particular claims – which ended at the close of September. Nonetheless, the indictment's dismissal would activate a half-year extension for the justice department to refile the case.

Even so in that situation, his lawyers said it plans to contend the prosecution is past the deadline.

The decision further indicates that because the charge is void, the statute of limitations has run and there can be no further indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In both decisions on the indictments against Comey and James, the judge was blunt: Halligan was wrongly appointed.

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

As a result, she lacked legal power to file the charges, she wrote.

Federal prosecutors are nominated by the US president and need US Senate confirmation. Federal statutes regulate how people can be appointed on a temporary basis, but the judge determined that Halligan's assignment had violated these regulations.

That leaves Halligan's position on subsequent cases against James and Comey, again, uncertain.

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

But Attorney General Bondi said on Monday that she designated Halligan a special federal prosecutor and commended her work as outstanding.

The White House stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.