I'm not sure. Some programs don't care if the EXE is renamed. I don't know enough about how SH3 is programmed to know if it will work or not. Change it, try to boot up the game, if it boots and works the EXE name is not important. If it doesn't just change it back.
If you're running any mods that require a copy of the EXE to be inside a folder inside the MODS folder (like HSIE patch) then make sure to change that EXE to the same name.
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