 Raynolds spent two months recovering from illness after the Valley Campaign, then was assigned as chief engineer of Middle Department and VIII Corps in January 1863. Promoted to major in the Corps of Engineers, he found himself in charge of the defenses of vital Harpers Ferry, West Virginia in March 1863 during Robert E. Lee's second Confederate invasion of the north during the Gettysburg Campaign. On March 31, 1863, the Corps of Topographical Engineers ceased to be an independent branch of the army and was merged into the Corps of Engineers and Raynolds served in that branch of the army for the remainder of his career. Officers from the two corps maintained their ranks based on the time at which they received their promotion.
