In a stark new illustration of the seemingly never-ending troubles of the system of war crimes courts at Guantanamo Bay, a federal civilian court on Tuesday nullified nearly 500 orders that had been issued by a military judge there because of ethical lapses.

The ruling by a three-judge panel of the U.S. Court of Appeals for the D.C. Circuit will mean that a high-profile case involving terrorism charges will basically have to re-start, with some three-and-a-half years of effort now scrapped.

“We fully recognize,” the court said in a 31-page opinion, “the burden [it was imposing] on the government, the public, and [the accused individual] himself,” but “we cannot permit an appearance of partiality to infect a system of justice that requires the most scrupulous conduct from its adjudicators, for the appearance of bias demeans the reputation and integrity not just of one jurist, but of the larger institution of which he or she is a part.”

The case involves a Saudi Arabian national, Abdul Al-Rahim Hussein Muhammad Al-Nashiri, who faces the death penalty if convicted on charges of plotting the bombing of a U.S. warship, the U.S.S. Cole in a harbor in Yemen in 2000, and other war crimes. Although his case has been unfolding for years at Guantanamo, it is still in the pre-trial stages, with no firm indication when it might go to an actual trial.

The military commission system at Guantanamo, first ordered into existence by President George W. Bush soon after the terrorist attack on the United States on September 11, 2001, and twice modified by acts of Congress, has had few convictions resulting or withstanding appeals. President Obama while in office sought to close down Guantanamo, but Congress refused to allow that. No new prisoners were sent there during Obama’s eight years in office. President Trump has ordered that the military prison stay open and that the military courts continue, and has vowed to send new terrorist suspects there, but so far there have been no new transfers to Guantanamo.

Tuesday’s ruling in the Al-Nashiri case was the third by the D.C. Circuit in his case, and marked the second time that the same court had ruled that a military judge involved in Guantanamo cases should have taken himself off of a case for ethical reasons.

The presiding judge in Al-Nashiri’s case, now-retired Air Force Colonel Vance Spath, has since taken a job as an immigration case judge at the Justice Department. The D.C. Circuit concluded that he had pursued that post with an agency that was a party in the Guantanamo case while handling the Al-Nashiri case, and did not make his dual role known to the defense lawyers or to the accused.

In a stern rebuke not only of Colonel Spath, but also of his superiors in the Pentagon, Justice Department officials and lawyers, and the military appeals court that reviews verdicts and other key court rulings at Guantanamo, the panel warned the federal government in general to take more care in monitoring the ethics of judges on the military courts.  However, it did not order any changes in how those judges are selected or assigned to cases at Guantanamo.

Although the Circuit Court rejected a plea by Al-Nashiri’s lawyers to dismiss the case against him, the panel did decide to nullify some 460 written orders he had issued and a number of oral rulings he had made from the bench. Last year, a federal civilian judge had nullified one of Spath’s more controversial rulings, holding a Marine general in contempt of court – and sending him temporarily to house arrest — for giving defense lawyers permission to leave the case after they had discovered possible spying on their meetings at Guantanamo with Al-Nashiri to talk about his defense.

Besides casting aside all orders Colonel Spath had issued since November 19, 2015, the Tuesday decision also wiped out any actions by the U.S. Court of Military Commission Review as it reviewed appeals from the military judge’s orders. That included orders seeking to force two civilian Pentagon lawyers who sought to leave the defense team for Al-Nashiri because of their concern over intrusions into their defense of the accused prisoner.

At one point, the trial judge had ordered three defense lawyers to be arrested and forced to go to Guantanamo to resume defending Al-Nashiri. In clearing those lawyers Tuesday, by wiping out orders against them, the Circuit Court implied that state bar rules that might have potentially threatened their legal licenses not be pursued, although it had no authority to explicitly prevent that from happening.