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Two well-known critics of President Trump obtained significant court wins on the start of the week when a federal judge threw out the federal indictments against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have insisted vehemently 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 attorney Lindsey Halligan's invalid assignment as US attorney. But she also left open the possibility for the government to try again.

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Comey acknowledged that likelihood after the decision, stating he believes Trump will probably come after him again.

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

But the DOJ faces steep obstacles to successfully prosecute both after this setback, and legal analysts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

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

Might the DOJ appeal?

The Department of Justice can contest Judge Currie's ruling 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, pledging to use all legal means, including an immediate appeal.

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

Abbe Lowell, James's lawyer, vowed to continue to challenge any further politically driven indictments through all legal avenues.

In the event of an appeals process, the DOJ probably would have its own attorneys present the arguments, making Halligan's involvement in the appeal uncertain.

Could there be new charges?

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

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

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

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

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

It's clear that it will be strongly disputed, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is appointed and is able to secure an indictment.

He described the tangle of attorneys, judges, and legal filings involved as a procedural morass with no easy solutions.

It could be harder for the DOJ to try to bring the exact same charges against James Comey.

A key issue is the legal time limit – the time frame that prosecutors had to charge him for these specific allegations – which ended at the end of September. However, the dismissal of the charges would trigger a half-year extension for the DOJ to refile the case.

Still in that case, his lawyers said it intends to argue the government is past the deadline.

The ruling also suggests that because the charge is invalid, the statute of limitations has expired and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

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

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

As a result, Halligan lacked legal power to file the charges, she wrote.

US attorneys are proposed by the US president and need US Senate confirmation. US laws govern how people can be appointed on a temporary 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, once more, uncertain.

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

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

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