After returning to service upon the apparent recovery from his wound, Scales participated in the campaigns of the Army of Northern Virginia during 1864 including the Wilderness, Spotsylvania Court House, and the Siege of Petersburg. Due to his previous wounds being unhealed, Scales took a leave of absence late in the war, and was at home in North Carolina when the army surrendered at Appomattox Court House. There is no record that the general was ever formally paroled, but he applied for amnesty at Raleigh on June 22, 1865, and was pardoned on June 18, 1866.