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Two high-profile critics 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, former FBI Director James Comey and New York Attorney General Letitia James have maintained vehemently that they are innocent, claiming that the administration and DOJ are merely singling out them for retaliation.

Federal Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's improper appointment as US attorney. However, she left the door open for the government to try again.

• Court throws out cases against former FBI chief Comey and NY attorney general James
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Comey acknowledged that possibility after the ruling, saying he thinks Trump will probably target him again.

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

But the government faces significant obstacles to effectively try either after this defeat, and legal analysts hesitate to forecast what could happen next due to the cases' unprecedented nature.

It feels to me like uncharted territory, said Professor Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

The DOJ 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 signaled she would take this route, vowing to use all legal means, including an expedited appeal.

In other cases, the former administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes fast-tracking its petitions up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any additional politically driven indictments through every lawful means available.

If there is an appeals process, the DOJ likely would have its own attorneys present the arguments, making Halligan's involvement in the appeals process unclear.

Is it possible there be new charges?

The federal prosecutors accused Comey with lying to Congress and obstruction of justice. Government lawyers charged James with bank fraud and providing false information to a financial institution.

Both pleaded not guilty. Besides claiming Halligan was unlawfully appointed, they also claimed to be targets of vindictive prosecution.

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

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, stated Ms Levine.

But John Day, head of the American College of Trial Lawyers, said it could be a complex process – 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 able to secure an indictment.

He characterized the tangle of attorneys, courts, 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 James Comey.

One problem is the legal time limit – the deadline that prosecutors had to indict Comey for these specific allegations – which expired at the end of September. However, the dismissal of the charges would activate a six-month grace period for the DOJ to refile the case.

Still in that situation, his lawyers said it intends to contend the prosecution is out of time.

The decision further indicates that since the charge is invalid, the statute of limitations has run and there can be no further indictment, attorney Patrick Fitzgerald said on Monday.

What is the fate of prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, Judge Currie was direct: Halligan's appointment was improper.

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

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

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

This makes Halligan's position on subsequent cases against both individuals, once more, unclear.

The ruling also could 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 made Halligan a special federal prosecutor and praised her work as outstanding.

The administration maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.