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Two high-profile critics of former President Trump achieved 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, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted vehemently that they are not guilty, asserting that the president and justice department are simply singling out them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's improper assignment as federal prosecutor. However, she left the door open for the federal authorities to try again.

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Comey acknowledged that likelihood after the ruling, stating he believes the former president will probably target him once more.

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

But the government confronts steep hurdles to successfully prosecute either after this setback, 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 Kay Levine, law professor at Emory University.

Might the DOJ challenge the ruling?

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

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

Previously, the Trump administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes fast-tracking its petitions up to the Supreme Court.

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically driven indictments through every lawful means available.

If there is an appeal, the DOJ likely would have its own attorneys present the arguments, making Halligan's involvement in the appeal unclear.

Is it possible there be new charges?

The government accused James Comey with making false statements to lawmakers and obstruction of justice. Federal prosecutors indicted Letitia James with bank fraud and providing false information to a financial institution.

Each pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, they also asserted to be victims of retaliatory legal action.

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

Based on my analysis, a new prosecutor could present James's case to a new grand jury and get a fresh indictment, said Professor Levine.

But John Day, president 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 strongly disputed, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an charge.

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

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

A key issue is the legal time limit – the time frame that government lawyers had to charge him for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the DOJ to bring the case again.

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

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

What happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against Comey and James, Judge Currie was blunt: Halligan was wrongly appointed.

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

As a result, Halligan had no lawful authority to file the charges, the judge wrote.

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

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

The decision might also raise doubts on other cases Halligan has prosecuted in the Virginia Eastern District where she serves.

But Bondi said on that day that she made Halligan a special US attorney and commended her work as excellent.

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