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

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have insisted fiercely that they are innocent, claiming that the administration and DOJ are simply singling out them for revenge.

Federal Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's invalid assignment as US attorney. However, she left the door open for the federal authorities to try again.

• Court throws out charges against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have compromised the Comey trial
• What is former FBI head James Comey charged with?

Comey acknowledged that likelihood after the decision, stating he thinks Trump will probably target him again.

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

But the DOJ faces steep hurdles to successfully prosecute either after this setback, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, stated Professor Kay Levine, Emory University School of Law professor.

Could the justice department challenge the ruling?

The Department of Justice can contest Judge Currie's ruling 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, vowing to use all legal means, including an immediate appeal.

Previously, the Trump administration has aggressively appealed adverse decisions, moving cases from lower courts and sometimes accelerating its petitions up to the Supreme Court.

Attorney Abbe Lowell, an attorney representing James, vowed to keep fighting any additional politically driven indictments 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 involvement in the appeals process unclear.

Is it possible there be fresh indictments?

The government accused Comey with lying to lawmakers and obstructing justice. Government lawyers indicted James with financial fraud and providing false information to a financial institution.

Both pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, both also claimed to be targets of vindictive prosecution.

Since the initial charges were dismissed (although appeals might alter this), the DOJ might try to assemble fresh grand juries and obtain new indictments.

Based on my analysis, 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 – certainly in Comey's case.

I can tell you it will be strongly disputed, whether Comey's case can be recharged if a properly assigned attorney is assigned and is able to secure an indictment.

He characterized the tangle of lawyers, courts, and motions involved as a legal quagmire with no easy solutions.

It could be harder for the government to try to file the identical accusations against James Comey.

A key issue is the statute of limitations – the deadline that government lawyers had to indict Comey for these particular claims – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the justice department to refile the case.

Still in that situation, his lawyers said it intends to argue 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 new indictment, attorney Patrick Fitzgerald said Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, Judge Currie was direct: Halligan was wrongly appointed.

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

As a result, Halligan had no lawful authority to present the indictment, the judge wrote.

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

That leaves Halligan's role on subsequent cases against James and Comey, 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 Attorney General Bondi said on that day that she designated her a special federal prosecutor and praised her work as excellent.

The White House maintained its position that Halligan was lawfully appointed, press secretary Karoline Leavitt told reporters on Monday.