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A pair of well-known critics of President Trump secured major court wins on Monday when a US judge dismissed the federal indictments against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have insisted vehemently that they are innocent, asserting that the administration and DOJ are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's improper assignment as federal prosecutor. But she also left the door open for the government to refile the case.

• Court throws out charges against ex-FBI director Comey and New York AG James
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Comey admitted that possibility after the decision, stating he believes Trump is likely to come after him again.

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

But the government confronts significant 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 unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

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

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

In other cases, the Trump administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes fast-tracking its petitions up to the US Supreme Court.

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

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

Could there be fresh indictments?

The government charged Comey with lying to Congress and obstructing justice. Federal prosecutors charged Letitia James with financial fraud and providing false information to a bank.

Each pleaded not guilty. In addition to 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 DOJ might try to assemble new grand juries and secure new charges.

Based on my analysis, a different attorney could present James's case to a different grand jury and secure a new indictment, stated 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.

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

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

It might be more difficult for the DOJ to try to bring the exact same charges against James Comey.

A key issue is the legal time limit – the deadline that government lawyers had to charge Comey for these specific allegations – which expired at the close of September. However, the indictment's dismissal would activate a six-month grace period for the DOJ to bring the case again.

Even so in that situation, his legal team said it intends to argue the government is past the deadline.

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

What is the fate of prosecutor Lindsey Halligan?

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

Judge Currie wrote in the James ruling that the AG's effort to install Halligan as Interim US Attorney for the Virginia Eastern District was invalid.

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

US attorneys are nominated by the US president and need Senate approval. US laws regulate how people can be appointed on a temporary basis, but Judge Currie found that Halligan's appointment had violated these regulations.

That leaves Halligan's role on future cases against both individuals, once more, uncertain.

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

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

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