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A pair of high-profile opponents of former President Trump obtained major court wins on the start of the week when a federal judge dismissed the government's charges against them.

Over recent weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have insisted fiercely that they are innocent, asserting that the president and justice department are simply targeting them for retaliation.

US District Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid appointment as US attorney. But she also left open the possibility for the federal authorities to refile the case.

• Judge dismisses charges against former FBI chief Comey and New York AG James
• Federal judge states DOJ errors may have compromised the Comey trial
• What is former FBI head James Comey charged with?

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

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

But the government faces steep obstacles to effectively try either after this defeat, and legal analysts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Kay Levine, law professor at Emory University.

Might the DOJ appeal?

The DOJ can challenge the judge's decision before a federal appeals court. In this case, that would be the Fourth Circuit Appeals Court.

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

Previously, the former administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its petitions up to the Supreme Court.

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

In the event of an appeals process, the justice department likely would have its own attorneys present the arguments, making Halligan's involvement in the appeal unclear.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with making false statements to Congress and obstruction of justice. Government lawyers indicted Letitia James with financial fraud and making false statements to a financial institution.

Both entered not guilty pleas. Besides claiming Halligan's appointment was invalid, both also asserted to be targets of vindictive prosecution.

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

As far as everything I've seen, a different attorney could present James's case to a different grand jury and get a fresh indictment, said Ms Levine.

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – especially in the Comey matter.

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a lawfully appointed prosecutor is appointed and is can obtain an indictment.

He described the tangle of lawyers, judges, and motions involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to file the exact same charges against Comey.

One problem is the statute of limitations – the deadline that prosecutors had to indict Comey for these particular claims – which ended at the close of September. Nonetheless, the indictment's dismissal would activate a six-month grace period for the DOJ 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 charge is invalid, the statute of limitations has expired and there can be no new indictment, attorney Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

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

The judge stated in the James ruling that the Attorney General's attempt to appoint Halligan as Interim US Attorney for the Virginia Eastern District was unlawful.

Therefore, Halligan lacked legal power to present the indictment, the judge wrote.

US attorneys are proposed by the president and need US Senate confirmation. US laws govern how individuals can be assigned on a interim basis, but the judge determined that Halligan's assignment had violated these laws.

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

The decision might also cast a shadow on any other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

But Bondi said on Monday that she designated Halligan a special federal prosecutor and commended her work as excellent.

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