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Two high-profile opponents of President Trump obtained major 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, ex-FBI chief James Comey and New York Attorney General Letitia James have maintained fiercely that they are not guilty, asserting that the president and justice department are simply singling out them for revenge.

US District Judge Cameron Currie dismissed the charges in their cases due to attorney Lindsey Halligan's improper appointment as US attorney. But she also left open the possibility for the government to try again.

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Comey admitted that likelihood after the ruling, saying he thinks Trump will probably target him again.

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

But the DOJ confronts significant hurdles to successfully prosecute either after this setback, and legal analysts are reluctant to predict what could occur next due to the unprecedented circumstances of the cases.

It feels to me like unexplored legal ground, stated Kay Levine, law professor at Emory University.

Could the DOJ challenge the ruling?

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

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

In other cases, the Trump administration has aggressively appealed adverse decisions, taking cases from trial courts and sometimes accelerating its requests up to the US Supreme Court.

Abbe Lowell, an attorney representing James, vowed to continue to challenge any additional politically driven indictments through all legal avenues.

In the event of an appeal, the DOJ probably would have its own attorneys present the arguments, making Halligan's role in the appeal uncertain.

Could there be new charges?

The federal prosecutors accused Comey with lying to Congress and obstruction of justice. Government lawyers indicted James with financial fraud and providing false information to a bank.

Both pleaded not guilty. Besides claiming Halligan's appointment was invalid, they also asserted to be targets of retaliatory legal action.

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

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

But John Day, president of the American College of Trial Lawyers, said it could be a complex process – certainly in Comey's case.

It's clear that it will be hotly contested, whether Mr Comey's case can be re-indicted if a properly assigned attorney is appointed and is can obtain an charge.

He described the complex web of attorneys, courts, and legal filings involved as a procedural morass with no easy solutions.

It could be harder for the government to try to bring the identical accusations against James Comey.

A key issue is the statute of limitations – the deadline that prosecutors had to charge Comey for these specific allegations – which ended at the close of September. However, the indictment's dismissal would activate a six-month grace period for the DOJ to refile the case.

Still in that situation, his lawyers said it intends to contend the prosecution is out of time.

The ruling also suggests that since the indictment is invalid, the statute of limitations has run and there can be no new 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 ruling that the AG's effort to appoint Halligan as Acting US Attorney for the Virginia Eastern District was invalid.

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

US attorneys are nominated by the president and require US Senate confirmation. Federal statutes govern how people can be assigned on a temporary basis, but the judge determined that Halligan's assignment had breached these regulations.

This makes Halligan's position on future cases against both individuals, again, uncertain.

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

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

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