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

For weeks since their indictments, former FBI Director James Comey and New York Attorney General Letitia James have maintained vehemently that they are not guilty, asserting that the administration and DOJ are merely singling out them for revenge.

Federal Judge Cameron Currie tossed the charges in their cases due to attorney Lindsey Halligan's improper assignment as US attorney. But she also left the door open for the federal authorities to try again.

• Court throws out charges against former FBI chief Comey and NY attorney general James
• Federal judge states DOJ errors may have compromised Comey case
• What are former FBI head James Comey charged with?

Comey acknowledged that possibility after the ruling, saying he believes the former president is likely to target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This will not be the last chapter on this issue.

But the DOJ faces significant hurdles to successfully prosecute either after this setback, and experts are reluctant to forecast what could occur next due to the cases' unprecedented nature.

It feels to me like unexplored legal ground, said Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

The DOJ can challenge Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Court of Appeals.

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

In other cases, the Trump administration has aggressively appealed unfavourable rulings, taking cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, James's lawyer, pledged to continue to challenge any additional politically motivated charges through every lawful means available.

In the event of an appeal, the DOJ likely would have its own lawyers argue the case, making Halligan's role in the appeal unclear.

Is it possible there be fresh indictments?

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

Each pleaded not guilty. Besides arguing Halligan's appointment was invalid, they also asserted to be targets of vindictive prosecution.

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

Based on my analysis, a new prosecutor could present James's case to a different grand jury and get a new 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 strongly disputed, whether Comey's case can be re-indicted if a properly assigned attorney is appointed and is able to secure an indictment.

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

It might be harder for the DOJ to try to bring the identical accusations against James Comey.

A key issue is the statute of limitations – the time frame that prosecutors had to charge him for these particular claims – which ended at the end of September. Nonetheless, the indictment's dismissal would trigger a six-month grace period for the justice department to refile the case.

Still in that case, his lawyers said it intends 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 Lindsey Halligan?

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

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

As a result, she lacked legal power to present the indictment, the judge wrote.

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

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

The ruling also could cast a shadow on other cases Halligan has prosecuted in the Eastern District of Virginia where she works.

But Attorney General Bondi said on that day that she made her a special federal prosecutor and commended her work as outstanding.

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