Level.dat files gone missing

My worlds randomly disappear from the singleplayer world list. Upon further inspection, the level.dat files seem to be gone.

I have attached 2 worlds where it has happened, with SHTUFF being the latest.

What happens
Level.dat files getting removed

What should happen
They should stay

To reproduce
1. Load up world
2. play around in it
3. Close the game with the X
4. ???
5. level.dat file is gone.