Complex sentence: The greater part of the history of the shrine, its origins and the miracles which were said to have occurred there, were lost in the sixteenth century when the chapel was suppressed in the Reformation and fell into ruin.
Split into simpler sentences: The greater part of the history of the shrine, its origins and the miracles which were said to have occurred there, have been lost in the destruction which came upon it in the sixteenth century. The chapel was suppressed in the Reformation and fell into ruin.