This article was produced in partnership with the Pulitzer Center on Crisis Reporting.

GUANTÁNAMO BAY, Cuba — A federal appeals court on Tuesday threw out more than two years of a military tribunal judge’s decisions in the case of the man accused of plotting the bombing of the destroyer Cole, finding that the jurist wrongly hid his pursuit of an immigration judge job while sitting on the war crimes case.

The decision by the United States Court of Appeals for the District of Columbia Circuit was a major setback in the oldest death-penalty case at Guantánamo Bay, and yet another twist in a winding and fraught case that has come to symbolize the government’s difficulties in pursuing prosecutions of detainees through the military tribunal system.

Abd al-Rahim al-Nashiri, 54, who has been in American custody since 2002, has been represented by military commission defense lawyers since 2008 and was formally charged in 2011. Mr. al-Nashiri, a Saudi, is accused of being the architect of Al Qaeda’s suicide bombing of the Navy destroyer Cole off Yemen on Oct. 12, 2000. Seventeen American sailors died, and dozens more were wounded.

But more than seven years after Mr. al-Nashiri’s arraignment, the case is still in pretrial hearings to determine what law and evidence would apply at a capital trial by the military commission. The decision means a new military judge will have to revisit defense challenges to the charges, what evidence prosecutors must provide Mr. al-Nashiri’s lawyers and fundamental constitutional questions about the legality of the military commission system.