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The far zone keeps the game's projection when a shader pack is loaded. A pack reads the depth buffer to work out where a pixel is in the world; the far zone wrote depth through a projection of its own, so parts of it were lit and shadowed as if they were somewhere else - dark smears with the world showing through. It now draws with the game's own projection and is cut off at the game's far plane, which is past the pack's fog anyway. Without a pack nothing changes.
Chunks edited while the server was down are noticed. Afterimage 0.6.1 snapshots the write times in the region file headers next to its change log, so a world edited from the outside (a script that fills an ocean, moves a city, rewrites biomes) is recorded as changed and clients drop the far copies they still hold of it.