Were there any disasters that happened to Mission San Luis Rey?

Answer 1

No, well not nearly as bad as some of the other missions. As you are aware the mission in San Juan, the next one to the north, was serious destroyed in the earthquake of 1812 (which some have estimated to be a 9.0+ on the Richter scale). San Juan was also invaded by pirates, which San Luis Rey escaped. San Diego, the next mission to the south, was beset at times by Indian uprisings, one of which killed at least one of the padres.

San Luis Rey was called the "King of the Missions" and was perhaps the richest of the them all. They controlled an incredible 16,000 cattle, 25,500 sheep and 2,150 horses graced the far-flung ranchos. 395,000 bushels of grain and 2,500 barrels of wine were produced by that same year (in 1831).

Perhaps the greatest disaster that happened to the mission occurred after the dissolution of the missions, or the secularization of the missions when the church was left to fall apart and suffer decades of deterioration and vandalism. It was restored until the very later 1890s and early 1900s.