He was charged and convicted at court martial on three counts of disobeying orders (when ordered by his superior to report), one count of dereliction of duty and one count of missing movement. He was allowed to present a defense, but was not allowed to challenge the eligibility of POTUS. Allowing any servicemember to challenge the authority of POTUS would be ridiculous, and create chaos and widespread insubordination.
He didn’t challenge the authority of POTUS. He challenged whether combat orders to Afghanistan were authorized by a Constitutional Commander in Chief as required by the Authorization to Use Force. The only thing that would make those orders lawful is if they were authorized by a Constitutional Commander in Chief. If Obama was not eligible to be the Commander in Chief then there was nobody in a position who could have lawfully ordered troops to Afghanistan under the Authorization to Use Force. Hence, all orders involving the movement of troops to Afghanistan would be unlawful.
Judge Denise Lind said “we don’t need no steenkin’ President to authorize combat operations in foreign countries.”