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Two prominent opponents of President Trump achieved major court wins on Monday when a US judge dismissed the federal indictments filed against them.

For weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have insisted vehemently that they are innocent, claiming that the president and justice department are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the charges against them due to attorney Lindsey Halligan's improper appointment as federal prosecutor. But she also left open the possibility for the government to try again.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
• US judge says government 'missteps' may have tainted the Comey trial
• What are former FBI head James Comey charged with?

Comey acknowledged that likelihood after the decision, saying he believes Trump will probably target him once more.

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

But the DOJ faces steep obstacles to effectively try either after this defeat, and experts hesitate to forecast what could happen next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Kay Levine, Emory University School of Law professor.

Could the DOJ appeal?

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

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

In other cases, the former administration has strongly challenged adverse decisions, taking cases from trial courts and sometimes accelerating its requests up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed 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 lawyers present the arguments, making Halligan's involvement in the appeals process unclear.

Is it possible there be new charges?

The federal prosecutors charged Comey with lying to lawmakers and obstruction of justice. Government lawyers charged James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, they 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 obtain new charges.

As far as everything I've seen, a new prosecutor could present James's case to a new grand jury and secure a fresh indictment, stated Ms Levine.

But 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 Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an charge.

He characterized the complex web of attorneys, courts, and legal filings involved as a procedural morass with no easy solutions.

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

One problem is the statute of limitations – the deadline that prosecutors had to charge Comey for these particular claims – which expired at the close of September. However, the dismissal of the charges would activate a half-year extension for the DOJ to refile the case.

Even so in that case, his lawyers said it intends to contend the government is past the deadline.

The decision further indicates that since the indictment is void, the time limit has run and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

In the pair of rulings on the charges against Comey and James, the judge was blunt: Halligan's appointment was improper.

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

As a result, she lacked legal power to present the indictment, the judge wrote.

US attorneys are proposed by the president and need Senate approval. Federal statutes govern how individuals can be appointed on a temporary basis, but Judge Currie found that Halligan's appointment had violated these laws.

This makes Halligan's position on future cases against both individuals, once more, unclear.

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

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

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