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Two high-profile critics of President Trump achieved major legal victories on the start of the week when a US judge threw out the government's charges filed against them.

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued fiercely that they are innocent, claiming that the administration and DOJ are simply targeting them for retaliation.

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

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Comey acknowledged that likelihood after the decision, saying he thinks the former president will probably target him again.

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

But the DOJ confronts steep obstacles to effectively try both after this setback, and legal analysts hesitate to predict what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Kay Levine, Emory University School of Law professor.

Could the DOJ challenge the ruling?

The DOJ can contest Judge Currie's ruling 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, pledging to use all available legal action, including an expedited appeal.

In other cases, the former administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes accelerating its petitions up to the US Supreme Court.

Abbe Lowell, James's lawyer, pledged to keep fighting any additional politically driven indictments through every lawful means available.

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

Is it possible there be fresh indictments?

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

Each pleaded not guilty. Besides arguing Halligan's appointment was invalid, they also asserted to be targets of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the government might try to convene new grand juries and secure new charges.

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

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – 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 can obtain an charge.

He characterized the tangle of attorneys, courts, and legal filings involved as a procedural morass with no simple answers.

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

One problem is the statute of limitations – the deadline that prosecutors had to charge Comey for these specific allegations – which ended at the close of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the DOJ to refile the case.

Still in that case, his lawyers said it plans to argue the government is out of time.

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

What happens to prosecutor Lindsey Halligan?

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

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

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

US attorneys are proposed by the president and require US Senate confirmation. US laws regulate how people can be appointed on a temporary basis, but the judge determined that Halligan's appointment had violated these regulations.

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

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

But Bondi said on Monday that she made Halligan a special federal prosecutor and praised her work as outstanding.

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