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

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

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's improper appointment as US attorney. However, she left open the possibility for the federal authorities to try again.

• Judge dismisses cases against former FBI chief Comey and NY attorney general James
• US judge says government 'missteps' may have tainted the Comey trial
• What is former FBI head James Comey accused of?

Comey acknowledged that likelihood after the decision, saying he thinks Trump is likely to target him once more.

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

But the DOJ faces significant hurdles to effectively try either after this defeat, and experts are reluctant to predict what could happen next due to the unprecedented circumstances of the cases.

It feels to me like uncharted territory, said Kay Levine, Emory University School of Law professor.

Could the justice department appeal?

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

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

In other cases, the former administration has strongly challenged adverse decisions, taking cases from lower courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, pledged to keep fighting any further politically driven indictments through every lawful means available.

If there is an appeals process, the justice department probably would have its own attorneys argue the case, making Halligan's role in the appeals process unclear.

Is it possible there be new charges?

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

Each pleaded not guilty. In addition to claiming Halligan was unlawfully appointed, both also claimed to be victims of retaliatory legal action.

With the original indictments thrown out (although appeals might alter this), the government might try to convene new grand juries and secure new indictments.

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

But John Day, head 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 recharged if a properly assigned attorney is assigned and is can obtain an indictment.

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

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

A key issue is the legal time limit – the time frame that government lawyers had to charge him for these specific allegations – which ended 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.

Even so in that situation, his lawyers said it plans to argue the prosecution is out of time.

The ruling also suggests that since the charge is invalid, the time limit has run and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of prosecutor Lindsey Halligan?

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

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

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

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

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

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

But Bondi said on that day that she made Halligan a special federal prosecutor and praised her work as outstanding.

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