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Two well-known opponents of President Trump obtained major court wins on the start of the week when a US judge threw out the government's charges filed against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued fiercely that they are innocent, claiming that the administration and DOJ are merely singling out them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's improper assignment as US attorney. However, she left open the possibility for the federal authorities to refile the case.

• Judge dismisses charges against ex-FBI director Comey and NY attorney general James
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• What is ex-FBI director James Comey charged with?

Comey admitted that likelihood after the decision, stating he thinks the former president will probably come after him once more.

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the final word on this issue.

But the DOJ confronts steep obstacles to successfully prosecute either after this defeat, and experts hesitate to forecast what could happen next due to the cases' unprecedented nature.

In my view, it's uncharted territory, stated Professor Kay Levine, Emory University School of Law professor.

Might the DOJ challenge the ruling?

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

US Attorney General Pam Bondi indicated she would pursue this option, pledging to use all legal means, including an immediate appeal.

In other cases, the former administration has aggressively appealed unfavourable rulings, moving cases from trial courts and sometimes accelerating its requests 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.

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

Is it possible there be new charges?

The federal prosecutors accused James Comey with making false statements to lawmakers and obstruction of justice. Federal prosecutors indicted James with financial fraud and making false statements to a financial institution.

Each entered not guilty pleas. In addition to claiming Halligan's appointment was invalid, both also asserted to be targets of retaliatory legal action.

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

Based on my analysis, a different attorney could bring James' case to a different grand jury and get a fresh indictment, stated Ms Levine.

But John Day, president 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 hotly contested, whether Mr Comey's case can be recharged if a properly assigned attorney is appointed and is able to secure an charge.

He described the complex web of lawyers, courts, and legal filings involved as a procedural morass with no easy solutions.

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

A key issue is the legal time limit – the time frame that prosecutors had to indict Comey for these particular claims – which ended at the close of September. However, the indictment's dismissal would activate a six-month grace period for the DOJ to refile the case.

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

The decision further indicates that since the indictment is void, the time limit has run 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, the judge was blunt: Halligan was wrongly appointed.

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

Therefore, Halligan lacked legal power to file the charges, she wrote.

US attorneys are proposed by the president and need US Senate confirmation. Federal statutes govern how people can be assigned on a temporary basis, but the judge determined that Halligan's appointment had violated these regulations.

This makes Halligan's role on subsequent cases against both individuals, once more, uncertain.

The decision might also raise doubts on other cases Halligan has brought in the Eastern District of Virginia where she works.

But Bondi said on Monday that she designated her a special federal prosecutor and commended her work as excellent.

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