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A pair of prominent opponents of President Trump achieved significant court wins on the start of the week when a US judge dismissed the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have maintained vehemently that they are innocent, asserting that the president and justice department are simply targeting them for retaliation.

US District Judge Cameron Currie tossed the charges against them due to attorney Lindsey Halligan's improper appointment as US attorney. However, she left the door open for the federal authorities to try again.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey acknowledged that likelihood after the ruling, stating he believes Trump is likely to come after him once more.

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

But the government faces steep hurdles to effectively try both after this defeat, and legal analysts 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 justice department challenge the ruling?

The Department of Justice can challenge Judge Currie's ruling before a federal appeals court. In this case, that would be the Fourth Circuit Court of Appeals.

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

In other cases, the Trump administration has strongly challenged adverse decisions, moving cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Abbe Lowell, James's lawyer, pledged to continue to challenge any additional politically driven indictments through all legal avenues.

If there is an appeals process, the justice department likely would have its own attorneys argue the case, making Halligan's involvement in the appeal uncertain.

Is it possible there be fresh indictments?

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

Both entered not guilty pleas. Besides claiming 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 assemble fresh grand juries and secure new indictments.

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

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – especially in the Comey matter.

It's clear that it will be strongly disputed, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an charge.

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

It might be harder for the DOJ to try to bring the exact same charges against Comey.

A key issue is the legal time limit – the time frame that prosecutors had to charge him for these particular claims – which ended at the end of September. However, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Even so in that situation, his lawyers said it plans to contend the prosecution is past the deadline.

The ruling also suggests that since the indictment is void, the time limit has run and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against James and Comey, the judge was blunt: Halligan was wrongly appointed.

Judge Currie wrote in the James ruling that the Attorney General's attempt to appoint Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

As a result, Halligan had no lawful authority to present the indictment, the judge wrote.

Federal prosecutors are proposed by the US president and require US Senate confirmation. US laws govern how people 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 subsequent cases against both individuals, again, unclear.

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

But Attorney General Bondi said on that day that she made Halligan a special federal prosecutor and commended her work as excellent.

The administration maintained its position that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.