Upon returning to the Shenandoah Valley, Augusta County voters again elected Harper to the Virginia House of Delegates, where he served until 1864. On June 2 of that year, after abolitionist Union General David Hunter's raid into the Shenandoah Valley, Harper accepted re-appointment as a colonel in the Confederate Army in order to form a regiment from reservist companies located in the Shenandoah Valley. During the Valley Campaigns of 1864 under General Jubal Early, Confederate raiders destroyed Harper's original hometown, Chambersburg, Pennsylvania on July 30, 1864 in retaliation for Hunter's campaign as well as its failure to pay ransom. However, Union forces continued to attack the Shenandoah valley. Col. Harper and his troops (under General Early) were routed at the Battle of Piedmont on June 5–6, 1864 and then the Battle of Waynesboro, Virginia on March 2, 1865.