So I understand why it was done, but forcefully ending a run if a save is loaded twice is a bad design choice.
I'm playing this on an emulator, and there are COUNTLESS times where for whatever reason, due to the emulator resetting or being closed, a save file is loaded twice. It's really frustrating to lose a strong run because of technical issues.
The thing is it doesn't even stop cheaters really. You can just use save states to circumvent the system entirely. I don't use save states because I don't want to cheat, and I'm being punished for that.
If people are going to cheat, they're gonna do it anyway. There's no reason to police that within the game itself.