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Two high-profile opponents of President Trump secured significant legal victories on the start of the week when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued vehemently that they are not guilty, claiming that the administration and DOJ are simply singling out them for revenge.

Federal Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid appointment as US attorney. But she also left open the possibility for the federal authorities to refile the case.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• US judge says government 'missteps' may have compromised Comey case
• What are ex-FBI director James Comey charged with?

Comey acknowledged that possibility after the ruling, saying he thinks Trump is likely to target him once more.

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

But the government confronts steep obstacles to successfully prosecute both after this setback, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Might the justice department 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.

US Attorney General Pam Bondi indicated she would pursue this option, pledging to use all legal means, including an expedited appeal.

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

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

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

Is it possible there be new charges?

The federal prosecutors charged Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted James with financial fraud and making false statements to a financial institution.

Each pleaded not guilty. Besides arguing Halligan was unlawfully appointed, they also claimed to be victims of retaliatory legal action.

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

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

But John Day, head 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 hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He described the complex web of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

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

One problem is the legal time limit – the time frame that government lawyers had to indict him for these specific allegations – which ended at the close of September. However, the dismissal of the charges would activate a six-month grace period for the DOJ to bring the case again.

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

The ruling also suggests that since the charge 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 both decisions on the indictments against James and Comey, the judge was blunt: Halligan's appointment was improper.

The judge stated in the James ruling that the Attorney General's attempt to install Ms. Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

Therefore, she had no lawful authority to present the indictment, she wrote.

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

That leaves Halligan's position on subsequent cases against James and Comey, once more, uncertain.

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

But Bondi said on that day that she designated Halligan a special federal prosecutor and commended her work as outstanding.

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.