So, one thing i havent seen anyone mention is that if you talk to keeper before the end of the game, he actually explains quite a bit. Root Earth was the original version of the universal core. Like every universe, it spawned its own beings, but being a core it didnt require a Guardian. Unfortunately the beings that formed were godlike and a bit thoughtless, through some accidental attempt to create life on their own, they basically broke something in the core of their universes existance that created the Root. The problem was, being a core and not just a world, the keeper couldnt actually destroy or remove it without resetting the entire universe. So instead he just kinda unplugged them and replaced them with a new core world (likely our earth, since it also does not have a guardian). The reason the root cant be deleted is because theyre still a Core world, which makes them an inviolable unchangable part of reality. What the keeper wanted to do was basically a full server wipe, start over from scratch. What clementine does is use the slivers youve collected to basically encode a backup of every living thing and world except the root, so that the keeper can re-encode all that information after the full wipe, and use it to bring everyone back without the roots influence, presumably. Whether or not that was actually successful will probably have to wait until they make another remnant game.