Ok, so, I tried opening 2 instances of the game and it didn't erase my savefile. Can you please go in detail? Also, try checking your savefile in User/AppData/Roaming/Spamton_Subplot
I'm not sure how to access that file, I opened the game files and all I could find was the Music, data.win, font, configuration settings, and the application.
Try researching on how to get into your AppData folder. It's useful in general. I'm just really interested on what kind of bug is this since several people mentioned something like this yet this never happened to me.