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Two prominent critics of former President Trump achieved major court wins on the start of the week when a US judge threw out the government's charges filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, asserting that the president and justice department are simply singling out them for retaliation.

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

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have compromised Comey case
• What are former FBI head James Comey accused of?

Comey admitted that possibility after the ruling, saying he thinks Trump is likely to come after him again.

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

But the DOJ faces steep hurdles to effectively try both after this setback, and legal analysts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, said Professor Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

The Department of Justice can challenge the judge's decision 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 legal means, including an immediate appeal.

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

Abbe Lowell, James's lawyer, pledged to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's role in the appeal unclear.

Is it possible there be new charges?

The federal prosecutors accused James Comey with lying to lawmakers and obstruction of justice. Government lawyers charged Letitia James with bank fraud and making false statements to a financial institution.

Each entered not guilty pleas. Besides claiming Halligan's appointment was invalid, they also claimed to be targets of retaliatory legal action.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to assemble new grand juries and secure new charges.

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

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – 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 able to secure an charge.

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

It might be harder for the DOJ to try to file the identical accusations against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to indict Comey for these specific allegations – which expired at the close of September. Nonetheless, the indictment's dismissal would activate a half-year extension for the DOJ to refile the case.

Still in that case, his lawyers said it intends to contend the government is out of time.

The ruling also suggests that since the charge is invalid, the statute of limitations has expired and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

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

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

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

Federal prosecutors are proposed by the president and need 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 role on subsequent cases against both individuals, once more, uncertain.

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

But Bondi said on that day that she made her a special US attorney and praised her work as outstanding.

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