Actually, I tried it again and it worked. I deleted them in-game like you said, closed the game, then I deleted all the config files where the .hki files are kept. I then validated the game using Steam and restarted the game, moving the desired hotkey files into the hotkey folder, and changed to that hotkey file in-game from the menu. This let me use the grid layout I had been using again.
I will not attempt to mess with the hotkeys again until this issue is fixed.