Hi CholericKolle!
Thanks for sending me the save files, the issue seam to do with a corrupted save file AutoSave1.ss, I am unsure what caused the corruption; I will further investigate.
The reason for your saves disappearing from the load menu was due to the fact that the game could not read the corrupted file, I will work on skipping over such files so in the future the game can carry on in case a file got corrupted somehow.
Quick fix is just to delete the AutoSave1.ss file and you are good to go.