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A pair of well-known critics of former President Trump obtained significant court wins on Monday when a federal judge threw out the government's charges against them.

Over recent weeks following their charges, former FBI Director James Comey and NY AG Letitia James have insisted vehemently that they are innocent, asserting that the president and justice department are simply singling out them for revenge.

Federal Judge Cameron Currie dismissed the indictments in their cases due to prosecutor Lindsey Halligan's invalid assignment as US attorney. However, she left the door open for the government to refile the case.

• Court throws out charges against ex-FBI director Comey and New York AG James
• Federal judge states DOJ errors may have compromised the Comey trial
• What are former FBI head James Comey charged with?

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

And White House spokesperson Abigail Jackson appeared to agree: This will not be the final word on this issue.

But the government faces significant obstacles to effectively try either after this setback, and experts are reluctant to predict 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 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 signaled she would pursue this option, vowing to use all legal means, including an immediate appeal.

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

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

If there is an appeals process, the DOJ likely would have its own lawyers argue the case, making Halligan's involvement in the appeal unclear.

Could there be new charges?

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

Both entered not guilty pleas. Besides claiming Halligan's appointment was invalid, they also claimed to be targets of vindictive prosecution.

Since the initial charges were dismissed (though, of course, appeals could change that), the DOJ might try to assemble new grand juries and obtain new charges.

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

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

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

He characterized the complex web of attorneys, judges, and legal filings involved as a legal quagmire with no simple answers.

It might be more difficult for the DOJ to try to file the exact same charges against Comey.

One problem is the statute of limitations – the time frame that government lawyers had to charge him for these particular claims – which ended at the end of September. Nonetheless, the indictment's dismissal would activate a half-year extension for the DOJ to refile the case.

Even so in that case, his lawyers said it plans to argue the government 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, attorney Patrick Fitzgerald said on Monday.

What happens to prosecutor Lindsey Halligan?

In the pair of rulings on the indictments against Comey and James, Judge Currie was direct: Halligan's appointment was improper.

The judge stated in the James ruling that the Attorney General's attempt to install Ms. Halligan as Interim US Attorney for the Eastern District of Virginia was unlawful.

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

US attorneys are proposed by the president and require Senate approval. US laws govern how people can be appointed on a temporary basis, but the judge determined that Halligan's assignment had breached these laws.

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

The decision might also cast a shadow on other cases Halligan has brought in the Virginia Eastern District where she serves.

But Attorney General Bondi said on that day that she made Halligan 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.