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A pair of prominent opponents of President Trump obtained major legal victories on the start of the week when a federal judge threw out the government's charges filed against them.

For weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted fiercely that they are innocent, asserting that the president and justice department are simply targeting them for retaliation.

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

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Comey acknowledged that possibility after the ruling, saying he thinks the former president will probably target him again.

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

But the government confronts steep obstacles to effectively try both after this defeat, and experts 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, law professor at Emory University.

Could the DOJ appeal?

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

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

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

Attorney Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically motivated charges through all legal avenues.

If there is an appeals process, the DOJ likely would have its own lawyers argue the case, making Halligan's involvement in the appeal unclear.

Could there be fresh indictments?

The federal prosecutors accused James Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted Letitia James with bank fraud and providing false information to a financial institution.

Both entered not guilty pleas. Besides arguing Halligan's appointment was invalid, both 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 new grand juries and secure new charges.

Based on my analysis, a new prosecutor could bring James' case to a new grand jury and secure 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.

It's clear that 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 characterized the tangle 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 bring the exact same charges against Comey.

One problem is the legal time limit – the deadline that government lawyers had to charge him for these specific allegations – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a six-month grace period for the DOJ to bring the case again.

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

The decision further indicates that because 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 both decisions on the indictments against James and Comey, the judge was direct: Halligan's appointment was improper.

The judge stated in the James ruling that the AG's effort to install Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

US attorneys are nominated by the president and require US Senate confirmation. US laws regulate how people can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had breached these laws.

That leaves Halligan's position on subsequent cases against both individuals, once more, uncertain.

The decision might also raise doubts on other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

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

The White House stood by its stance that Halligan was lawfully appointed, spokesperson Karoline Leavitt told reporters on Monday.