Well, one could always imagine the church had control of the stone. Perhaps it was a spoil of war or considered a relic. Mathias simply procured it, perhaps illegally.
Or, Mathias' family might have protected it. It's suggested that his family is powerful, knowledgeable, and using more alchemy could have masked the existence of the stone to anyone or anything that would have sought it.
Subsequently, when Elizabeth dies, Mathias has only to search the family inventory.