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Two high-profile opponents of former President Trump obtained significant legal victories on the start of the week when a US judge threw out 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 not guilty, asserting that the administration and DOJ are simply targeting them for revenge.

US District Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. But she also left the door open for the federal authorities to refile the case.

• Court throws out cases against ex-FBI director Comey and NY attorney general James
• Federal judge states government 'missteps' may have compromised the Comey trial
• What are ex-FBI director James Comey accused of?

Comey admitted that possibility after the ruling, stating he thinks the former president will probably target him once more.

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

But the government faces steep obstacles to effectively try both after this defeat, and legal analysts hesitate to predict what could occur next due to the cases' unprecedented nature.

In my view, it's unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Could the DOJ challenge the ruling?

The DOJ can contest the judge's decision before a higher appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

US Attorney General Pam Bondi indicated she would pursue this option, 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 requests up to the Supreme Court.

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

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

Is it possible there be new charges?

The federal prosecutors charged James Comey with making false statements to lawmakers and obstructing justice. Federal prosecutors indicted Letitia James with bank 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 vindictive prosecution.

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

Based on my analysis, a new prosecutor could present James's case to a different grand jury and get a fresh indictment, stated Ms Levine.

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

I can tell you it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an charge.

He described the complex web of attorneys, judges, and motions involved as a legal quagmire with no easy solutions.

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

One problem is the legal time limit – the time frame that government lawyers had to indict him for these specific allegations – which expired at the end of September. Nonetheless, the indictment's dismissal would trigger a half-year extension for the DOJ to bring the case again.

Even so in that case, his legal team said it intends to argue the government is out of time.

The decision further indicates that because the indictment is void, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

In both decisions on the indictments against Comey and James, the judge was blunt: Halligan's appointment was improper.

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

As a result, Halligan lacked legal power to file the charges, the judge wrote.

US attorneys are proposed by the US president and need US Senate confirmation. US laws govern how individuals can be appointed on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

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 prosecuted in the Virginia Eastern District 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 White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.