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Two well-known opponents of President Trump obtained major court wins on the start of the week when a federal judge dismissed the federal indictments against them.

Over recent weeks following their charges, former FBI Director James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the president and justice department are merely singling out them for revenge.

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

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Comey admitted 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 isn't the last chapter on this matter.

But the DOJ confronts significant hurdles to effectively try both after this setback, and legal analysts hesitate to predict what could happen next due to the unprecedented circumstances of the cases.

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 federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

US Attorney General Pam Bondi signaled she would take this route, pledging to use all available legal action, including an immediate appeal.

In other cases, the Trump administration has strongly challenged adverse decisions, taking cases from lower courts and sometimes accelerating its petitions up to the US Supreme Court.

Attorney Abbe Lowell, an attorney representing James, pledged to continue to challenge any further politically motivated charges through all legal avenues.

In the event of an appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's involvement in the appeal unclear.

Is it possible there be new charges?

The federal prosecutors charged Comey with lying to Congress and obstructing justice. Federal prosecutors charged James with bank fraud and making false statements to a bank.

Both entered not guilty pleas. Besides claiming Halligan's appointment was invalid, both also claimed to be targets of vindictive prosecution.

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

As far as everything I've seen, a different attorney could present James's case to a new grand jury and secure a new indictment, stated Ms Levine.

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

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

He described the tangle of lawyers, courts, and legal filings involved as a procedural morass with no simple answers.

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

A key issue is the statute of limitations – the time frame that government lawyers had to indict him for these particular claims – which expired at the end of September. However, the dismissal of the charges would trigger a six-month grace period for the DOJ to refile the case.

Still in that situation, his legal team said it intends to argue the government is past the deadline.

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

What is the fate of prosecutor 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 appoint Ms. Halligan as Acting US Attorney for the Eastern District of Virginia was unlawful.

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

Federal prosecutors are proposed by the US president and need Senate approval. US laws regulate how people can be appointed on a interim basis, but the judge determined that Halligan's appointment had violated these regulations.

That leaves Halligan's position on future cases against James and Comey, once more, unclear.

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

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

The White House stood by its stance that Halligan was lawfully appointed, press secretary Karoline Leavitt told the press on Monday.