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A pair of prominent opponents of President Trump obtained major court wins on the start of the week when a US judge threw out the government's charges against them.

For weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have maintained fiercely that they are not guilty, asserting that the president and justice department are simply singling out them for retaliation.

US District Judge Cameron Currie tossed the charges against them due to attorney Lindsey Halligan's invalid assignment as US attorney. However, she left open the possibility for the federal authorities to refile the case.

• Court throws out cases against former FBI chief Comey and New York AG James
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Comey admitted that possibility after the ruling, stating he thinks Trump is likely to come after him once more.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the final word on this issue.

But the government faces steep hurdles 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.

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

Could the justice department appeal?

The DOJ can challenge Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

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

Previously, the former administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

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

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

Is it possible there be new charges?

The government accused James Comey with lying to Congress and obstruction of justice. Government lawyers charged James with financial fraud and making false statements to a bank.

Each pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, they also claimed to be targets of vindictive prosecution.

With the original indictments thrown out (although appeals might alter this), the government might try to convene new grand juries and obtain new charges.

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

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

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 can obtain an indictment.

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

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

One problem is the legal time limit – the time frame that prosecutors had to charge Comey for these specific allegations – which expired at the close of September. However, the dismissal of the charges would activate a half-year extension for the DOJ to refile the case.

Still in that case, his legal team said it plans to contend the government is out of time.

The ruling also suggests that because the indictment is void, the statute of limitations has run and there can be no new indictment, attorney Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against Comey and James, the judge was blunt: Halligan was wrongly appointed.

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

As a result, she lacked legal power to present the indictment, the judge wrote.

Federal prosecutors are nominated by the president and require Senate approval. US laws govern how people can be assigned on a interim basis, but the judge determined that Halligan's assignment had breached these regulations.

This makes Halligan's role on subsequent cases against James and Comey, once more, unclear.

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

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

The White House maintained its position that Halligan was lawfully appointed, spokesperson Karoline Leavitt told reporters on Monday.