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Two well-known critics of President Trump obtained major legal victories on Monday when a US judge threw out the federal indictments filed against them.

For weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, asserting that the president and justice department are merely targeting them for revenge.

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

• Court throws out charges against former FBI chief Comey and New York AG James
• Federal judge states DOJ errors may have compromised Comey case
• What is ex-FBI director James Comey charged with?

Comey admitted that likelihood after the ruling, saying he thinks Trump is likely to come after him again.

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

But the government confronts significant obstacles to successfully prosecute either after this setback, and legal analysts hesitate to forecast what could happen next due to the unprecedented circumstances of the cases.

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

Might the DOJ challenge the ruling?

The Department of Justice can challenge the judge's decision before a higher appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

Previously, the Trump administration has strongly challenged unfavourable rulings, moving cases from lower courts and sometimes fast-tracking its requests up to the Supreme Court.

Abbe Lowell, James's lawyer, vowed to keep fighting any further politically motivated charges through every lawful means available.

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

Could there be new charges?

The government accused Comey with making false statements to lawmakers and obstructing justice. Federal prosecutors indicted James with financial 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.

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

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

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

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is assigned and is can obtain an indictment.

He described the tangle of lawyers, judges, and motions involved as a procedural morass with no simple answers.

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

A key issue is the statute of limitations – the deadline that government lawyers had to charge Comey for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the justice department to bring the case again.

Still in that case, his lawyers said it intends to contend the government is past the deadline.

The decision further indicates that since 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 prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, the judge was blunt: Halligan's appointment was improper.

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

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

Federal prosecutors are nominated by the US president and require Senate approval. Federal statutes regulate how people can be appointed on a temporary basis, but the judge determined that Halligan's appointment 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 designated 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.