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

Over recent weeks following their charges, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained fiercely that they are innocent, asserting that the administration and DOJ are merely singling out them for retaliation.

Federal Judge Cameron Currie tossed the charges against them due to attorney Lindsey Halligan's improper appointment as federal prosecutor. However, she left the door open for the federal authorities to try again.

• Judge dismisses charges against former FBI chief Comey and New York AG James
• Federal judge states government 'missteps' may have tainted the Comey trial
• What are ex-FBI director James Comey charged with?

Comey admitted that possibility after the decision, saying he thinks Trump is likely to come after him again.

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

But the government confronts steep hurdles to effectively try either after this setback, and legal analysts hesitate 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 higher appeals court. In this case, that would be the Fourth Circuit Appeals Court.

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

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

Attorney Abbe Lowell, an attorney representing James, vowed to continue to challenge any further politically driven indictments through every lawful means available.

In the event of an appeal, the justice department likely would have its own attorneys present the arguments, making Halligan's role in the appeals process unclear.

Is it possible there be fresh indictments?

The federal prosecutors charged James Comey with lying to Congress and obstruction of justice. Government lawyers charged James with bank fraud and making false statements to a financial institution.

Each pleaded not guilty. Besides arguing Halligan's appointment was invalid, they 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 assemble new grand juries and secure new indictments.

Based on my analysis, a different attorney could present James's case to a new grand jury and secure a fresh indictment, stated Professor Levine.

But John Day, head of the American College of Trial Lawyers, said it could be a complicated path – certainly in the Comey matter.

It's clear that it will be strongly disputed, whether Comey's case can be re-indicted if a lawfully appointed prosecutor is assigned and is able to secure an charge.

He described the tangle of attorneys, judges, and legal filings involved as a legal quagmire with no easy solutions.

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

One problem is the legal time limit – the deadline that prosecutors had to charge him for these particular claims – which ended at the close of September. Nonetheless, the dismissal of the charges would activate a half-year extension for the justice department to bring the case again.

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

The ruling also suggests that because the indictment is void, the statute of limitations has run and there can be no new indictment, lawyer Patrick Fitzgerald said Monday.

What happens to Lindsey Halligan?

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

Judge Currie wrote in the James ruling that the AG's effort to appoint Ms. Halligan as Interim US Attorney for the Virginia Eastern District was invalid.

Therefore, she lacked legal power to file the charges, she wrote.

US attorneys are proposed by the president and require Senate approval. US laws govern how individuals can be assigned on a interim 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 ruling also could raise doubts on any other cases Halligan has brought in the Virginia Eastern District where she serves.

But Bondi said on Monday that she made Halligan a special US attorney and praised her work as outstanding.

The White House stood by its stance that Halligan's appointment was legal, press secretary Karoline Leavitt told the press on Monday.