Earthquakes, Landslides, Rivers changing course over time and then shaping the landscape. Also just the ambient accumulation of topsoil from continual cycles of growth, death, and decomposition on the ruins (plant grow, plant die, plant dead matter eventually broken down by decomposers into basically just more dirt), winds bring in dust which while subtle and small can accumulate over time, especially when manmade structures provide areas for said dust to get stuck and out of the wind once brought in.
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