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Two prominent critics of former President Trump secured major legal victories on the start of the week when a federal judge threw out the federal indictments against them.

Over recent weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have argued fiercely that they are innocent, claiming that the president and justice department are merely targeting them for retaliation.

US District Judge Cameron Currie tossed the charges in their cases due to prosecutor 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 NY attorney general James
• Federal judge states DOJ errors may have compromised the Comey trial
• What is ex-FBI director James Comey charged with?

Comey admitted that likelihood after the decision, saying he thinks 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 DOJ confronts significant obstacles to effectively try both after this defeat, and experts are reluctant to forecast what could happen next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Kay Levine, law professor at Emory University.

Might the justice department appeal?

The DOJ can contest the judge's decision before a higher 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 available legal action, including an immediate appeal.

Previously, the Trump administration has strongly challenged unfavourable rulings, taking cases from trial courts and sometimes accelerating its petitions up to the US 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 argue the case, making Halligan's involvement in the appeal uncertain.

Is it possible there be fresh indictments?

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

Both entered not guilty pleas. In addition to arguing Halligan was unlawfully appointed, they also asserted to be victims of retaliatory legal action.

With the original indictments thrown out (though, of course, appeals could change that), the DOJ might try to convene fresh grand juries and secure new indictments.

Based on my analysis, a different attorney could bring James' case to a new grand jury and get 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 the Comey matter.

It's clear that it will be strongly disputed, whether Mr Comey's case can be re-indicted if a properly assigned attorney is assigned and is able to secure an indictment.

He characterized the tangle of attorneys, judges, and motions involved as a legal quagmire with no simple answers.

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

A key issue is the statute of limitations – the deadline that prosecutors had to indict Comey for these particular claims – which expired at the close of September. Nonetheless, the dismissal of the charges would trigger a half-year extension for the justice department to refile the case.

Even so in that situation, his legal team said it intends to contend the prosecution is out of time.

The decision further indicates that since the charge is void, the statute of limitations has expired and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What is the fate of Lindsey Halligan?

In both decisions on the charges against Comey and James, the judge was blunt: Halligan was wrongly appointed.

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

Therefore, she had no lawful authority to present the indictment, she wrote.

Federal prosecutors are nominated by the US president and require US Senate confirmation. US laws regulate how individuals can be assigned on a temporary basis, but Judge Currie found that Halligan's appointment had breached these regulations.

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

The decision might also raise doubts on any other cases Halligan has prosecuted in the Virginia Eastern District where she works.

But Bondi said on Monday that she designated Halligan 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.