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Two prominent critics of President Trump secured significant legal victories on the start of the week when a federal judge threw out the government's charges against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted vehemently that they are innocent, asserting that the administration and DOJ are merely targeting them for revenge.

US District Judge Cameron Currie dismissed the indictments against them due to attorney Lindsey Halligan's improper appointment as federal prosecutor. However, she left open the possibility for the government to try again.

• Court throws out charges against ex-FBI director Comey and NY attorney general James
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• What are former FBI head James Comey accused of?

Comey acknowledged that possibility after the decision, saying he believes the former president is likely to come after him once more.

And White House spokeswoman Abigail Jackson appeared to agree: This will not be the final word on this matter.

But the DOJ faces significant hurdles to effectively try either after this defeat, and experts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

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

Might the DOJ challenge the ruling?

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

Attorney General Pam Bondi signaled she would pursue this option, pledging to use all legal means, including an expedited appeal.

In other cases, the Trump administration has strongly challenged unfavourable rulings, moving cases from trial 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 every lawful means available.

In the event of an appeals process, the justice department likely would have its own lawyers argue the case, making Halligan's role in the appeal unclear.

Could there be fresh indictments?

The federal prosecutors charged Comey with making false statements to Congress and obstructing justice. Government lawyers charged Letitia James with financial fraud and providing false information to a bank.

Both entered not guilty pleas. In addition to claiming Halligan's appointment was invalid, they also asserted to be victims of retaliatory legal action.

Since the initial charges were dismissed (although appeals might alter this), the government might try to convene fresh grand juries and secure 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, said Professor Levine.

But John Day, president 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 re-indicted if a properly assigned attorney is assigned and is can obtain an charge.

He characterized the tangle of lawyers, judges, and motions involved as a legal quagmire with no simple answers.

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

One problem is the statute of limitations – the time frame that government lawyers had to indict him for these particular claims – which expired at the close of September. However, the indictment's dismissal would trigger a half-year extension for the DOJ to refile the case.

Even so in that situation, his legal team said it plans to argue the prosecution is out of time.

The ruling also suggests that because the indictment is void, the statute of limitations 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 James and Comey, the judge was blunt: Halligan's appointment was improper.

Judge Currie wrote in the James decision that the AG's effort to appoint Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

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

That leaves Halligan's position on future cases against James and Comey, once more, unclear.

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

But Attorney General Bondi said on that day that she made Halligan a special US attorney and praised her work as excellent.

The White House stood by its stance that Halligan's appointment was legal, spokesperson Karoline Leavitt told the press on Monday.