I've logged hours on a game (Earthbound) and just accidentally pressed F1, loading a save state from over a week ago, having no idea that it would automatically overwrite the .srm file. Well, I'm flabbergasted that a single button placed next to the often-used Escape could destroy my game progress, but I understand that I probably have no recourse, so I'll just ask: is there some option to keep this from happening in the future? I really, really like SNES9X, but I'm a bit frustrated here.

Yes, such an option would be nice. The same thing happened to me some time ago.

Yes, you can disable the hotkey, go to Input > Customize Hotkeys and click on the white box next to "load0", and press Esc. The white box should then say "Disabled".

Hopefully that will fix your issue.

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What operating system are you using? 32 or 64bit? Version of Snes9x? Is the text at the bottom of the window white when you load the game?
These suggestions are usually the solution to your issue!

If something like this happens look into the snapshot folder for a .oops file - this is a backup snapshot that is automatically created if you load or reset a game after playing more than five minutes without saving to a state.

If you've since played on this could have gotten overwritten, but you might be lucky.