My observations and theory
>!This is my theory about what the Daughter is/was. (haven't seen anyone propose this here yet, maybe I just didn't look hard enough)!<
>!I think the Daughter was the other moon of Apiary. The Axum say the Daughter "fell from space" but they don't say it fell too Proteus. !<
>!While the orrery model and description have some inconsistencies at this stage in the game's development, they both show that Apiary has more than one moon and no system of rings. (you can see a planet with a ring system further out in the orrery model and they don't look like the lines surrounding Apiary)!<
>!The observatory is supposed to be rebuilt from before the "drowning", reflecting the Eido-Thea system before the Daughter fell from space. If you look up at Apiary in game, you don't see any other moons, you do see a big ring system. !<
>!Proteus has a larger mass than Earth (1.05g) yet hasn't cleared this ring system, which means it was made recently (on an astronomical time scale). !<
>!Orbits decay slowly, and then all at once. Another moon of Apiary being ripped apart as it sank into the gas giant would have been devastating for Proteus. Large fragments would have impacted the surface and clouded the sky while smaller ones would have destroyed the Axum's orbital infrastructure and made spaceflight impossible for them. !<
>!This may explain why photosynthesis is uncommon on Proteus. While the nuclear winter has ended, the moon's ecology is still recovering from a period of little to no light reaching the surface. !<
>!This event likely triggered massive quakes, which would have injured the world trees' root systems. Titan rock bores would be able to recover from the occasional quake, but quakes and meteor impacts on that scale would have caused much more serious injury. !<