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A pair of high-profile opponents of President Trump achieved significant court wins on the start of the week when a federal judge dismissed the government's charges filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued fiercely that they are not guilty, asserting that the administration and DOJ are merely targeting them for retaliation.

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

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Comey acknowledged that possibility after the ruling, saying he thinks Trump will probably come after him once more.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the final word on this matter.

But the government confronts steep hurdles to effectively try either after this defeat, and experts are reluctant to forecast what could occur next due to the unprecedented circumstances of the cases.

In my view, it's uncharted territory, stated Professor Kay Levine, law professor at Emory University.

Might the DOJ challenge the ruling?

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

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

In other cases, the Trump administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes accelerating its petitions up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any additional politically motivated charges through all legal avenues.

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

Could there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to lawmakers and obstruction of justice. Government lawyers indicted James with bank fraud and making false statements to a bank.

Each pleaded not guilty. In addition to claiming Halligan's appointment was invalid, they also asserted to be victims of vindictive prosecution.

With the original indictments thrown out (though, of course, appeals could change that), the government might try to convene fresh grand juries and obtain new indictments.

As far as everything I've seen, a different attorney could present James's case to a different grand jury and secure a fresh indictment, stated Professor 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.

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

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

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

One problem is the legal time limit – the time frame that prosecutors had to charge Comey for these particular claims – which expired at the end of September. However, the indictment's dismissal would trigger a half-year extension for the justice department to refile the case.

Even so in that case, his lawyers said it intends to argue the prosecution is out of time.

The decision further indicates that because the charge is invalid, the time limit has run and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

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

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

Therefore, Halligan lacked legal power to file the charges, she wrote.

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

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

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

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

The administration stood by its stance that Halligan was lawfully appointed, spokesperson Karoline Leavitt told reporters on Monday.