The Sea of Flames was left behind in the grotto as Werner and Marie-Laure escaped Saint-Malo.
Marie-Laure believed that putting the Sea of Flames back into the ocean would break its curse. As she and Werner attempted to flee the city under siege, she placed the stone in the gated grotto. It's still in the wooden model that held it for so long. Then she asks Werner whether it's in the sea; he says it is. She locks the grotto and they continue to flee.
When they part ways, Marie-Laure gives Werner the key to the grotto. Years later, long after Werner has died, she finds the grotto key in the little model house that Werner went back to retrieve. Though she can't be sure that he never went to retrieve the stone, she thinks it was likely left in the grotto down among the snails on the ground.
The book confirms this in the "Sea of Flames" chapter, where it says:
Another hour, another day, another year. Lump of carbon no larger than a chestnut. Mantled with algae, bedecked with barnacles. Crawled over by snails. It stirs among the pebbles.