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

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

Federal Judge Cameron Currie dismissed the charges in their cases due to prosecutor Lindsey Halligan's invalid assignment as federal prosecutor. But she also left open the possibility for the federal authorities to try again.

• 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 are former FBI head James Comey charged with?

Comey admitted that possibility after the ruling, saying he thinks the former president is likely to target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This will not be the final word on this issue.

But the DOJ faces significant hurdles to effectively try both after this setback, and legal analysts hesitate to predict what could occur next due to the cases' unprecedented nature.

It feels to me like unexplored legal ground, said Kay Levine, law professor at Emory University.

Might the justice department appeal?

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

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

Previously, the Trump administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

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

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

Could there be new charges?

The federal prosecutors accused Comey with making false statements to Congress and obstruction of justice. Government lawyers indicted James with bank fraud and providing false information to a bank.

Each pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, they also claimed to be targets of vindictive prosecution.

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

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

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

It's clear that it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is able to secure an charge.

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

It could be harder for the DOJ to try to file the exact same charges against Comey.

A key issue is the legal time limit – the deadline that government lawyers had to indict him for these particular claims – which expired at the close of September. However, the dismissal of the charges would activate a six-month grace period for the justice department to refile the case.

Even so in that situation, his lawyers said it plans to contend the prosecution is out of time.

The decision further indicates that since the charge is void, the time limit has run and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

In both decisions on the charges against Comey and James, the judge was blunt: Halligan's appointment was improper.

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

Therefore, she had no lawful authority to file the charges, she wrote.

US attorneys are proposed by the US president and require US Senate confirmation. Federal statutes regulate how individuals can be assigned on a interim basis, but the judge determined that Halligan's appointment had violated these laws.

This makes Halligan's role on future cases against both individuals, once more, unclear.

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

But Attorney General Bondi said on Monday that she designated her a special US attorney and commended her work as excellent.

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