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A pair of high-profile critics of former President Trump secured major court wins on the start of the week when a federal judge dismissed the government's charges against them.

For weeks following their charges, ex-FBI chief James Comey and NY AG Letitia James have insisted vehemently that they are not guilty, claiming that the administration and DOJ are simply singling out them for retaliation.

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

• Court throws out 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 acknowledged that likelihood after the ruling, saying he believes the former president will probably come after him again.

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

But the government confronts significant obstacles to successfully prosecute both after this setback, and experts hesitate to predict what could occur next due to the unprecedented circumstances of the cases.

In my view, it's unexplored legal ground, said Professor Kay Levine, Emory University School of Law professor.

Might the DOJ appeal?

The DOJ can contest Judge Currie's ruling before a federal appeals court. In this instance, that would be the Fourth Circuit Appeals Court.

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

In other cases, the Trump administration has aggressively appealed adverse decisions, moving cases from trial courts and sometimes fast-tracking its petitions up to the US Supreme Court.

Attorney Abbe Lowell, James's lawyer, vowed to keep fighting any additional politically driven indictments through every lawful means available.

In the event of an appeals process, the justice department likely would have its own lawyers argue the case, making Halligan's involvement in the appeal unclear.

Is it possible there be fresh indictments?

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

Both pleaded not guilty. In addition to arguing Halligan's appointment was invalid, both also asserted to be targets of vindictive prosecution.

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

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

But legal expert John Day, president of the American College of Trial Lawyers, said it could be a complex process – certainly 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 appointed 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 could be harder for the government to try to file the identical accusations against James Comey.

A key issue is the legal time limit – the deadline that prosecutors had to charge Comey for these particular claims – which ended at the close of September. However, the indictment's dismissal would trigger a six-month grace period for the DOJ to refile the case.

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

The decision further indicates that because the indictment is void, the time limit has expired and there can be no further indictment, lawyer Patrick Fitzgerald said Monday.

What is the fate of Lindsey Halligan?

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

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

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

US attorneys are proposed by the US president and require US Senate confirmation. Federal statutes regulate how people can be assigned on a interim basis, but Judge Currie found that Halligan's assignment had violated these laws.

That leaves Halligan's position on future cases against James and Comey, again, 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 that day that she made her a special federal prosecutor and commended her work as excellent.

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