This usually happens only in some specific circumstances:
- When using a save file editor like PKHeX
- When using save states
- When using cheat codes
- When shutting down the emulation whilst you’re saving your game.
If any of these things caused your save file to become corrupted though, unless you have a Save State of your progress, there’s no way to recover the data. You’ll need to start over.
In order to delete your corrupted save file:
Start Citra, then right click on your game in Citra’s game list (you may need to add a game directory for your game first for it to show up here), then select
Open Save Data Location. Move up one folder in the file path (inside the “data” folder) and delete both the
00000001 folder as well as the metadata file found here. Now start your game again and you should be able to play your game again.