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A pair of prominent critics of President Trump achieved significant court wins on the start of the week when a federal judge dismissed the government's charges filed against them.

For weeks since their indictments, former FBI Director James Comey and NY AG Letitia James have maintained fiercely that they are innocent, claiming that the president and justice department are simply targeting them for revenge.

Federal Judge Cameron Currie dismissed the indictments against them due to prosecutor Lindsey Halligan's improper assignment as US attorney. But she also left the door open for the federal authorities to try again.

• Judge dismisses charges against ex-FBI director Comey and NY attorney general James
• Federal judge states DOJ errors may have compromised Comey case
• What are ex-FBI director James Comey charged with?

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

And White House spokesperson Abigail Jackson seemed to confirm it: This isn't the last chapter on this matter.

But the DOJ faces steep obstacles to effectively try either after this setback, 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, stated Professor Kay Levine, Emory University School of Law professor.

Could the DOJ appeal?

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

Attorney General Pam Bondi signaled she would take this route, vowing to use all available legal action, including an immediate appeal.

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

Abbe Lowell, James's lawyer, vowed to continue to challenge any additional politically motivated charges through all legal avenues.

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

Is it possible there be fresh indictments?

The federal prosecutors accused James Comey with making false statements to Congress and obstructing justice. Federal prosecutors indicted James with financial fraud and providing false information to a bank.

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

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

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

But legal expert John Day, head of the American College of Trial Lawyers, said it could be a complicated path – certainly in Comey's case.

I can tell you it will be hotly contested, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is can obtain an charge.

He characterized the tangle of attorneys, courts, and motions involved as a procedural morass with no easy solutions.

It could be harder for the DOJ 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 indict Comey for these specific allegations – which ended at the close of September. However, the indictment's dismissal would trigger a six-month grace period for the justice department to bring the case again.

Even so in that case, his legal team said it intends to contend the prosecution is past the deadline.

The ruling also suggests that since the indictment is invalid, 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 the pair of rulings on the charges against James and Comey, 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.

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

US attorneys are proposed by the US president and need Senate approval. Federal statutes govern how people can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had breached these regulations.

This makes Halligan's position on future cases against James and Comey, once more, uncertain.

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

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

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