The souls in the afterlives slowly dissipate and fuse with them, thus providing energy for the gods to help tide them over. However, I'd imagine there's a quick round of nuking to mop up any "squatters" (so to speak) who inexplicably are able to survive through the world's end by one means or another. And they also rework the world to match the new theme, so even if someone (and/or their family tree) endured that long they might not be compatible with the new physics.