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

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, asserting that the administration and DOJ are merely singling out them for revenge.

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

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Comey admitted that likelihood after the decision, stating he thinks the former president is likely to target him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the last chapter on this matter.

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

It feels to me like uncharted territory, stated Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

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 pursue this option, vowing to use all available legal action, including an immediate appeal.

Previously, the Trump administration has aggressively appealed adverse decisions, taking cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any further politically motivated charges through every lawful means available.

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

Could there be new charges?

The government charged Comey with making false statements to Congress and obstructing justice. Government lawyers indicted James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. Besides arguing Halligan's appointment was invalid, both 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 indictments.

As far as everything I've seen, a new prosecutor could bring James' case to a different 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 complex process – certainly in Comey's case.

I can tell you it will be strongly disputed, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is can obtain an charge.

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

It might be harder for the government to try to file the identical accusations against James Comey.

One problem is the statute of limitations – the time frame that prosecutors had to indict him for these particular claims – which ended at the end of September. However, the dismissal of the charges would activate a six-month grace period for the DOJ to refile the case.

Even so in that situation, his legal team said it plans to argue the prosecution is past the deadline.

The ruling also suggests that because the indictment is invalid, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

Judge Currie wrote 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 had no lawful authority to present the indictment, the judge wrote.

US attorneys are proposed by the president and need US Senate confirmation. Federal statutes govern how individuals can be appointed on a interim basis, but the judge determined that Halligan's appointment had breached these regulations.

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

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

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

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