I was having the same issue, but I think mine had to do with sleep vs shutdown. My computer would go to sleep instead of shutting down, then if it was shut off all the way and the sleep data was lost, every file in the save directory would be replaced with blank hex files. Cataclysm is not the only program that did this for me, claws mail kept losing it’s folder structure xml file in the same way.
I changed it so my comp never sleeps now and it seems to have fixed it. I still keep save backups just in case. If the issue comes back and this was just a red hearing, I will remember to post it here.