Thanks for your help. It seems my saves are safe.
I believe I've partially figured out the issue. It seems there is some code in the binary that requires that the filename not be changed. The default filename is "Neon" for some reason. If you change it to "Neon Struct" the game will crash on launch.
I still haven't been able to determine what is wrong with the icon. It was visible at some point but now it's not.