Modern versions of the patch use LayeredFS , allowing you to keep your original game files untouched while the custom firmware (CFW) loads the Japanese audio files on top.
If you encounter issues with DLC not loading, use the Luma3DS Locale Switcher to set the game's region to Japan, which sometimes fixes compatibility with undubbed files. Portable Play via Emulation (Citra) shin megami tensei iv apocalypse undub 3ds portable
Right-click the game in Citra, select "Open Custom Texture Location," and place the undubbed files there (ensure "Use Custom Textures" is enabled in graphics settings). Modern versions of the patch use LayeredFS ,