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

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

Federal Judge Cameron Currie dismissed the indictments in their cases due to attorney Lindsey Halligan's invalid assignment as US attorney. But she also 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
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• What are ex-FBI director James Comey charged with?

Comey admitted that likelihood after the decision, saying he thinks Trump is likely to come after him once more.

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

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

It feels to me like uncharted territory, said Kay Levine, law professor at Emory University.

Might the DOJ appeal?

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

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

In other cases, the former administration has strongly challenged unfavourable rulings, moving cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any further politically motivated charges through all legal avenues.

In the event of an appeal, the justice department probably would have its own lawyers argue the case, making Halligan's role in the appeal uncertain.

Is it possible there be fresh indictments?

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

Both entered not guilty pleas. Besides arguing 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 government might try to assemble 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 Professor Levine.

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complicated path – especially 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 assigned and is can obtain an indictment.

He described the complex web of lawyers, judges, and legal filings involved as a legal quagmire with no simple answers.

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

One problem is the statute of limitations – the time frame that government lawyers had to charge Comey for these specific allegations – which expired at the close of September. Nonetheless, the dismissal of the charges would activate a half-year extension for the justice department to refile the case.

Still in that case, his lawyers said it intends to contend the government 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 further indictment, lawyer Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

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

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

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

Federal prosecutors are nominated by the president and require US Senate confirmation. US laws regulate how people can be assigned on a temporary basis, but Judge Currie found that Halligan's appointment had violated these regulations.

This makes Halligan's position on future cases against both individuals, again, unclear.

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

But Attorney General Bondi said on that day that she made her a special US attorney and commended her work as outstanding.

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