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Two prominent opponents of President Trump achieved significant court wins on the start of the week when a federal judge threw out the federal indictments filed against them.

For weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have maintained fiercely that they are innocent, asserting that the administration and DOJ are simply targeting them for retaliation.

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

• Court throws out charges against former FBI chief Comey and New York AG James
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• What are former FBI head James Comey accused of?

Comey acknowledged that likelihood after the decision, saying he believes Trump is likely to come after him again.

And White House spokesperson Abigail Jackson seemed to confirm it: This will not be the final word on this issue.

But the DOJ faces significant hurdles to successfully prosecute either after this setback, and legal analysts are reluctant to predict what could happen next due to the cases' unprecedented nature.

It feels to me like unexplored legal ground, stated Kay Levine, law professor at Emory University.

Could the DOJ challenge the ruling?

The Department of Justice can challenge the judge's decision before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

Attorney General Pam Bondi indicated she would take this route, vowing to use all legal means, including an immediate appeal.

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

Attorney Abbe Lowell, James's lawyer, pledged to continue to challenge any further politically motivated charges through all legal avenues.

In the event of an appeals process, the DOJ probably would have its own lawyers present the arguments, making Halligan's role in the appeals process unclear.

Is it possible there be new charges?

The federal prosecutors charged Comey with making false statements to lawmakers and obstruction of justice. Government lawyers indicted Letitia James with financial fraud and providing false information to a bank.

Both pleaded not guilty. In addition to claiming Halligan's appointment was invalid, they also asserted to be victims of retaliatory legal action.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to convene fresh grand juries and obtain new charges.

As far as everything I've seen, a new prosecutor could bring James' case to a new grand jury and secure a fresh indictment, said 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.

It's clear that it will be hotly contested, whether Mr Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an indictment.

He characterized the complex web of lawyers, judges, and legal filings involved as a legal quagmire with no easy solutions.

It might be more difficult for the government to try to file the exact same charges against Comey.

A key issue is the legal time limit – the deadline that government lawyers had to indict Comey for these particular claims – which ended at the close of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the DOJ to bring the case again.

Still in that situation, his lawyers said it plans to contend the government is out of time.

The ruling also suggests that since the charge is void, the statute of limitations has run and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

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

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

Therefore, Halligan lacked legal power to present the indictment, the judge wrote.

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

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

The ruling also could raise doubts on other cases Halligan has brought in the Eastern District of Virginia where she serves.

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

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