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My save was fine until update v0.3.31.0, which I updated the same way as I always do, download the zip file and then replace the old version's files with the new. That is when the "Load" option on the Main Menu became the "Crash the game" option. 
I was able to "Continue" (loads the most recent save) from the Main Menu in v0.3.31.0, but when I hit a Game Over scenario it overwrote my Quick Save with an Auto save and has locked me out of the saves I have in the "Load" section.

And before you ask yes my saves are still in the saves folder after I replaced the other files. I've been able to view them as files on my computer but not in game because of the crash that occurs when trying to open that screen.

I could probably go back to a previous version of the game but that does not fix the issues I'm having with this version.  

I also posted in the  v0.3.31.0 update comments what the crash error message said to do. It seems to be some error reading something or other. I'm no programmer.