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Two high-profile opponents of President Trump secured major legal victories on the start of the week when a US judge dismissed the federal indictments against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have maintained vehemently that they are innocent, claiming that the president and justice department are simply targeting them for revenge.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. However, she left the door open for the federal authorities to try again.

• Judge dismisses charges against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have compromised Comey case
• What are former FBI head James Comey charged with?

Comey acknowledged that likelihood after the ruling, stating he thinks Trump is likely to come after him again.

And White House spokeswoman Abigail Jackson appeared to agree: This isn't the last chapter on this issue.

But the government faces significant obstacles to effectively try either after this defeat, and legal analysts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

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

Might the justice department challenge the ruling?

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

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

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

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

If there is an appeals process, the DOJ probably would have its own attorneys argue the case, making Halligan's role in the appeal uncertain.

Is it possible there be new charges?

The government charged James Comey with lying to Congress and obstruction of justice. Government lawyers indicted James with financial fraud and providing false information to a bank.

Both pleaded not guilty. Besides claiming Halligan was unlawfully appointed, they also claimed 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.

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

But 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 Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an indictment.

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

It could be more difficult for the government to try to bring the identical accusations against James Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to charge Comey for these particular claims – which expired at the close of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the DOJ to bring the case again.

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

The decision further indicates that because the charge is void, the time limit has expired and there can be no further indictment, attorney Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

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

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

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

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

This makes Halligan's role on future cases against James and Comey, once more, unclear.

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

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

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