WOLFSBURG, Germany—Two top Volkswagen engineers who found they couldn’t deliver as promised a clean diesel engine for the U.S. market are at the center of a company probe into the installation of engine software designed to fool regulators, according to people familiar with the matter. The two men, Ulrich Hackenberg, Audi ’s chief engineer, and Wolfgang Hatz, developer of Porsche’s winning Formula One engines, were among the engineers suspended in the investigation of the emissions cheating scandal that sank the company’s market value by 43% since Sept. 18 and triggered a world-wide recall to refit the engines to meet clear-air...