Eniam was untouched by the Clone Wars, but only months after the conflicts end, the new First Galactic Empire took Eniam. The Military fought hard but were eventually overwhelmed. Later in the Galactic Civil War the Empire had mostly forgotten the planet. Soon after the Battle of Endor, the natives easily overwhelmed the remaining garrison.
After that, the Military was reformed under the same name and command structure. However, Eniam's life was again pulled apart in the Yuuzhan Vong War. Years later, the military was reformed for a third time.