Finding replacements for soldiers captured or killed was difficult because, throughout the war, men were recruited by the states rather than the federal government.
Governors awarded colonel’s commissions to favored citizens who would round up recruits. Sometimes the regiments would go off to fight without their colonels.
It was easier politically to form a new regiment than to raise replacements, so much of the war was fought with skeleton regiments.
Source: The Army of the Potomac: Mr. Lincoln’s Army by Bruce Catton