On a PC, save files are typically found in your Citra "nand" directory, usually under AppData\Roaming\Citra\sdmc\Nintendo 3DS\00000000...\title\00040000\00160c00\data\00000001\ . How to Back Up and Transfer Your Save
If you are moving to a new console or want a safety backup, you have several options: project x zone 2 save file
For retail copies, your progress (levels, items, and story completion) is saved directly onto the Nintendo 3DS Game Card itself. On a PC, save files are typically found