I accidentally saved to the 3rd slot by mis-clicking (I use an emulator). Now I have two copies of the save. How do I delete the save I have on the 3rd slot? If it's not possible natively in-game, are there hacks I can do on the save file to remove it?
I don't think you can natively 'delete' the game save without erasing your current save slot as well.
As for a hack, I've never come across one for people to delete particular game saves (for any game). I daresay the emulator save file is a direct (S)RAM dump, and with the right tool you might be able to trial and error/ brute force remove it, but this would take time.
Other than that, you could try and find a friend (or a website) that has a save file for the level you are on, and download and use that.
Your best bet is to overwrite the extra save with a new game. It won't be blank, but at least it won't stand out