A divided federal appeals court on Friday threw out an agreement that would have allowed accused Sept. 11 mastermind Khalid Sheikh Mohammed to plead guilty in a deal sparing him the risk of execution for al-Qaida’s 2001 attacks. The decision by a panel of the federal appeals court in Washington, D.C., undoes an attempt to wrap up more than two decades of military prosecution beset by legal and logistical troubles. The deal, negotiated over two years and approved by military prosecutors and the Pentagon’s senior official for Guantanamo Bay, Cuba, a year ago, stipulated life sentences without parole for Mohammed and two co-defendants.