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A pair of high-profile opponents of President Trump obtained significant court wins on the start of the week when a federal judge threw out the government's charges against them.

Over recent weeks since their indictments, ex-FBI chief James Comey and New York Attorney General Letitia James have argued vehemently that they are innocent, claiming that the president and justice department are simply singling out them for retaliation.

Federal Judge Cameron Currie tossed the indictments in their cases due to prosecutor Lindsey Halligan's invalid appointment as US attorney. But she also left open the possibility for the government to try again.

• Court throws out cases against former FBI chief Comey and New York AG James
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Comey acknowledged that possibility after the decision, stating he believes Trump will probably come after him again.

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

But the government confronts steep hurdles to effectively try both after this setback, and legal analysts are reluctant to forecast what could happen next due to the cases' unprecedented nature.

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

Might the DOJ appeal?

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

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

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

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

If there is an appeal, the justice department probably would have its own attorneys argue the case, making Halligan's involvement in the appeals process uncertain.

Could there be fresh indictments?

The federal prosecutors accused Comey with lying to lawmakers and obstructing justice. Federal prosecutors indicted James with bank fraud and providing false information to a financial institution.

Both entered not guilty pleas. Besides arguing Halligan's appointment was invalid, both also asserted to be targets 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 obtain new indictments.

Based on my analysis, a different attorney could present James's case to a different 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.

I can tell you 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 complex web of attorneys, courts, and motions involved as a legal quagmire with no easy solutions.

It could be more difficult for the DOJ to try to file the identical accusations against Comey.

One problem is the statute of limitations – the deadline that government lawyers 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 bring the case again.

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

The ruling also suggests that because the indictment is invalid, the time limit has run and there can be no further indictment, lawyer Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In both decisions on the charges against Comey and James, the judge was direct: Halligan was wrongly appointed.

The judge stated in the James ruling that the Attorney General's attempt to install 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 nominated by the president and require US Senate confirmation. US laws govern how individuals can be appointed on a interim basis, but the judge determined that Halligan's assignment had breached these regulations.

That leaves Halligan's position on subsequent cases against both individuals, again, uncertain.

The ruling also could raise doubts on any other cases Halligan has brought in the Virginia Eastern District where she works.

But Attorney General Bondi said on Monday that she designated her a special federal prosecutor and commended her work as excellent.

The White House stood by its stance that Halligan was lawfully appointed, spokesperson Karoline Leavitt told the press on Monday.