That's a weird one! There's no updater in fleshcult itself, and the only code I wrote that handles deletion is for save files, so I can't think of anything it could be doing to nuke itself like that. If you're seeing exes vanish both in Steam and Itch it sure seems like there's some third party at work. Are they winding up in Avast's quarantine or something?
It might've had trouble starting because there are two executables involved: fleshcult.exe, which has the game logic, and subprocess.exe which has a browser engine that displays the game. If subprocess.exe got eaten, it won't be able to start.