Sylvester Bonnaffon, Jr. then re-enlisted for military service once again — this time with the Pennsylvania National Guard's 1st Regiment Infantry (also known as the "Gray Reserves"). After enlisting as a private on October 15, 1868 he was promoted to the rank of first lieutenant with Company H on March 2, 1870. Detailed as acting regimental adjutant in January 1871, he then served as captain of that same company from June 14, 1871 to September 14, 1872, and was honorably discharged on September 4, 1874. On October 4, 1875, he and his wife welcomed the twin births of his namesake son, Sylvester Bonnaffon, III (1875–1945) and Edmund Walters Bonnaffon (1875–1954). Like their father before them, both went on to pursue careers in the military. In 1877, his services were called upon again when multiple members of the PNG were mustered in to restore order during the Pittsburgh railroad strike. Commissioned as colonel and placed in charge of the 20th Regiment, which had been specially raised in response to the emergency, he led his troops from July through September, during which time his troops also helped to quell unrest between coal miners and other residents of Pennsylvania's Lehigh and Wyoming valleys, including within the cities of Scranton and Wilkes-Barre. Appointed as a major with the artillery of the Washington Grays, he served from March 22 to July 20, 1879, and was then re-commissioned as a colonel by the PNG on January 14, 1880. Placed in command of the Third Infantry Regiment, he held that position for exactly one decade. From 1890 until the time of his retirement on August 20, 1920, Bonnaffon was employed by the Customs House in Philadelphia, working his way up from positions as examiner and assistant cashier to cashier. Earlier that same year, he was preceded in death by his brother, Charles, a long-time jeweler in Philadelphia who was fatally burned in a fire on January 29, 1920, caused by smoking in bed. Sylvester Bonnaffon, Jr. died on May 12, 1922 in Philadelphia, Pennsylvania. Following funeral services on May 16 at the Church of the Transfiguration, he was laid to rest at The Woodlands Cemetery in Philadelphia. He was survived by his sons, Commander Edmund W. Bonnaffon and Captain Sylvester Bonnaffon, III, who both had served during World War I.