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The save file for Inazuma Eleven Go: Shadow is usually located in the game's data folder on your console or emulator. Here are the locations for different platforms: Inazuma Eleven Go Shadow Save File
Paste the downloaded save file contents into this directory. Restart Citra and boot up the game. How to Install a Save File on a Nintendo 3DS (Homebrew) I can provide or help you find the exact resources you need
Copy the existing files in that folder and paste them into a secure backup folder on your desktop. Inazuma Eleven Go Shadow Save File