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Two well-known critics of President Trump obtained significant court wins on Monday when a US judge threw out the government's charges filed against them.

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

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

• Court throws out cases against ex-FBI director Comey and New York AG James
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• What is ex-FBI director James Comey accused of?

Comey acknowledged that likelihood after the ruling, stating he believes Trump will probably come after him once more.

And White House spokesperson Abigail Jackson appeared to agree: This will not be the last chapter on this matter.

But the government confronts significant hurdles to effectively try both after this defeat, and experts hesitate to forecast what could happen next due to the cases' unprecedented nature.

It feels to me like unexplored legal ground, stated Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

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

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

Previously, the former administration has strongly challenged unfavourable rulings, taking cases from trial courts and sometimes accelerating its petitions up to the US 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 lawyers present the arguments, making Halligan's involvement in the appeal unclear.

Could there be fresh indictments?

The federal prosecutors accused Comey with making false statements to lawmakers and obstructing justice. Federal prosecutors indicted Letitia James with financial fraud and making false statements to a bank.

Each pleaded not guilty. In addition to arguing Halligan was unlawfully appointed, they also asserted to be victims of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the government might try to assemble new 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 new indictment, said Professor Levine.

But John Day, president of the American College of Trial Lawyers, said it could be a complicated path – especially in Comey's case.

It's clear that it will be hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is can obtain an indictment.

He characterized the complex web of attorneys, judges, and legal filings involved as a legal quagmire with no simple answers.

It could be more difficult for the government to try to file the identical accusations against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to charge him for these particular claims – which ended at the end of September. However, the indictment's dismissal would activate a six-month grace period for the DOJ to refile the case.

Still in that case, his legal team said it plans to contend the government is past the deadline.

The decision further indicates that since the charge is invalid, the time limit has run and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to Lindsey Halligan?

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

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

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

US attorneys are nominated by the president and need Senate approval. US laws govern how individuals can be assigned on a temporary basis, but the judge determined that Halligan's appointment had violated these laws.

That leaves Halligan's position on future cases against both individuals, once more, unclear.

The ruling also could cast a shadow on other cases Halligan has brought in the Virginia Eastern District where she serves.

But Bondi said on that day that she made Halligan a special US attorney and commended her work as outstanding.

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