Being that the exterior is some sort of stucco/earthen kind of material, it would have been refinished on the outside multiple times in 600 years. There's buildings around 800 years old where I live that are in great condition because they've been well maintained. Also it's pretty typical for old religious buildings to have been added onto and modified in phases. Quite a lot of the big old churches in Europe changed in design and grew in size over 100s of years, for example.