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A pair of high-profile critics of President Trump secured major legal victories on the start of the week when a US judge threw out the federal indictments against them.

For weeks since their indictments, ex-FBI chief James Comey and NY AG Letitia James have insisted vehemently that they are innocent, asserting that the president and justice department are merely targeting them for revenge.

US District Judge Cameron Currie tossed the indictments against them due to attorney Lindsey Halligan's invalid appointment as federal prosecutor. But she also left the door open for the federal authorities to try again.

• Judge dismisses cases against ex-FBI director Comey and NY attorney general James
• Federal judge states government 'missteps' may have tainted Comey case
• What is ex-FBI director James Comey charged with?

Comey admitted that possibility after the decision, saying he thinks the former president is likely to target him once more.

And White House spokesperson Abigail Jackson appeared to agree: This isn't the last chapter on this matter.

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

In my view, it's uncharted territory, stated Professor Kay Levine, law professor at Emory University.

Could the justice department appeal?

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

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

In other cases, the former administration has aggressively appealed adverse decisions, taking cases from lower courts and sometimes fast-tracking its petitions 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 appeals process, the justice department probably would have its own lawyers present the arguments, making Halligan's role in the appeals process uncertain.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to lawmakers and obstructing justice. Government lawyers charged James with financial fraud and providing false information to a financial institution.

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

With the original indictments thrown out (though, of course, appeals could change that), the government might try to assemble new grand juries and obtain new indictments.

Based on my analysis, a different attorney could bring James' case to a new grand jury and secure a new indictment, said Ms 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 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, judges, and legal filings involved as a legal quagmire with no easy solutions.

It might be harder for the government to try to file the exact same charges against James Comey.

A key issue is the statute of limitations – the time frame that government lawyers had to indict him for these specific allegations – which expired at the end of September. Nonetheless, the dismissal of the charges would activate a six-month grace period for the DOJ to refile the case.

Still in that situation, his legal team said it plans to contend the government is past the deadline.

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

What is the fate of prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, the judge was blunt: Halligan's appointment was improper.

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

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

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

This makes Halligan's role on future cases against both individuals, again, unclear.

The decision might also cast a shadow on other cases Halligan has brought in the Eastern District of Virginia where she works.

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

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