What happened to the Indian tribes after the mission was built?
The Indian Tribes in California suffered a severe decline population after the arrival of the Europeans. Diseases that they were not protected against (Smallpox, for example) had a devastating effect. Some Indians covered to Christianity, others escaped to the interior.
Ultimately the remnants of some of the tribes were put on reservations. The Pala Sub-mission (bout 25 miles east of San Luis Rey) is on an Indian Reservation and the church there is still serving the native american population.