San Luis Rey de Francia was secularized in 1834, and the buildings were stripped and abandoned in subsequent years. In 1846 some of the buildings were occupied by the U.S. Army during the Mexican American War. The famous Indian scout, Kit Carson was with the army detachment encamped at the mission. Even though San Luis Rey was returned to the Church in 1865 the mission was essentially abandoned between 1865-1892. During this time the quadrangle collapsed and portions of the church caved in.
A group of Mexican Franciscans from Zacatecas arrived in 1892, and began rebuilding the mission. Rebuilding continued well into the 20th century and still continues.
Restorers tried to use authentic materials and adhere to Fr. Antonio Peyri's original design but also, where necessary, they used materials that would meet modern safety standards. In 1926 a corner of the companario collapsed and had to be repaired, and I understand that reinforced concrete was used. During the reconstruction of the church the reredos had to be recreated without any pictures or drawings of the original, and the polychrome bultros were designed to fit with the neoclassical style of the side altars. Another example of reconstruction is the entrance and steps into the Lavanderia which were rebuilt using brick..