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A pair of high-profile opponents of former President Trump obtained significant court wins on the start of the week when a federal judge threw out the government's charges filed against them.

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, asserting that the president and justice department are merely targeting them for retaliation.

US District Judge Cameron Currie dismissed the indictments against them 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.

• Judge dismisses charges against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have tainted the Comey trial
• What is former FBI head James Comey accused of?

Comey acknowledged that possibility after the ruling, saying he believes the former president is likely to come after him again.

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

But the DOJ faces significant hurdles to effectively try either after this defeat, and legal analysts are reluctant 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 challenge the ruling?

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

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

Previously, the former administration has strongly challenged unfavourable rulings, taking cases from lower courts and sometimes accelerating its requests 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 appeal, the DOJ likely would have its own lawyers present the arguments, making Halligan's involvement in the appeals process unclear.

Could there be fresh indictments?

The government accused Comey with making false statements to lawmakers 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 arguing Halligan was unlawfully appointed, both also asserted to be targets of vindictive prosecution.

With the original indictments thrown out (though, of course, appeals could change that), the government might try to convene new grand juries and secure new charges.

As far as everything I've seen, a new prosecutor could present James's case to a different 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 complicated path – certainly in the Comey matter.

It's clear that it will be strongly disputed, whether Mr Comey's case can be recharged if a properly assigned attorney is assigned 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 DOJ to try to file the identical accusations against Comey.

One problem is the statute of limitations – the deadline that government lawyers had to charge Comey for these particular claims – which ended at the end of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the justice department to bring the case again.

Even so in that case, his lawyers said it intends to contend the prosecution is out of time.

The decision further indicates that since the charge 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 Lindsey Halligan?

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

Judge Currie wrote in the James decision that the Attorney General's attempt to install Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

Therefore, Halligan lacked legal power to present the indictment, the judge wrote.

Federal prosecutors are proposed by the US 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 violated these laws.

This makes Halligan's role on future cases against James and Comey, again, unclear.

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

But Attorney General Bondi said on Monday that she made Halligan a special federal prosecutor and commended her work as outstanding.

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