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

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have insisted vehemently that they are innocent, asserting that the president and justice department are merely targeting them for revenge.

US District Judge Cameron Currie tossed the charges against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. But she also left the door open for the government to refile the case.

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

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

But the government faces significant obstacles to effectively try either after this setback, and experts are reluctant to predict what could happen next due to the cases' unprecedented nature.

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

Could the DOJ challenge the ruling?

The DOJ can contest the judge's decision before a federal appeals court. In this case, that would be the Fourth Circuit Appeals Court.

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

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

Attorney Abbe Lowell, an attorney representing James, pledged to keep fighting any additional politically motivated charges through all legal avenues.

In the event of an appeals process, the justice department probably would have its own attorneys argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be fresh indictments?

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

Both pleaded not guilty. In addition to arguing Halligan's appointment was invalid, they also claimed to be victims of vindictive prosecution.

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

As far as everything I've seen, a different attorney could bring James' case to a different grand jury and get a new indictment, said Ms Levine.

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

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an charge.

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

It could be harder for the government to try to file the exact same charges against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to charge him for these particular claims – which ended at the close of September. However, the indictment's dismissal would activate a half-year extension for the DOJ to bring the case again.

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

The decision further indicates 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 happens to prosecutor Lindsey Halligan?

In both decisions on the indictments against James and Comey, Judge Currie was blunt: Halligan's appointment was improper.

Judge Currie wrote in the James ruling that the Attorney General's attempt to appoint Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

As a result, she had no lawful authority to file the charges, the judge wrote.

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

That leaves Halligan's position on future cases against both individuals, again, unclear.

The decision might also cast a shadow on any other cases Halligan has prosecuted in the Eastern District of Virginia where she serves.

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

The White House maintained its position that Halligan's appointment was legal, press secretary Karoline Leavitt told the press on Monday.