The Twelve are most likely not going to appear in the story again since Endwalker made a point of ending the story of Hydaelyn, Zodiark, and the ancients. The Twelve's influence on Etheirys remains due to the device they built, but they themselves have passed on. Their passing isn't going to have much of an effect on the setting since the only people who know that they're gone are keeping it a secret, because if the truth did get out, then people would stop praying, and the Twelve leaving behind the device to act in their stead would be for nothing.