I don't downgrade or upgrade versions, but my worlds keep disappearing nonetheless. This happened to me on two survival and a creative superflat world. When I went to my file explorer to copy the region data into a new world, the new world also vanished, and when I copied everything but the region data into the old world, I spawned in the void, then my game crashed.
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If you don't have a level.dat file, the world doesn't appear in the list, and if you don't have region data, the world can't generate. (Correct me if I'm wrong)