Does anyone know of a program for Windows that can explore RomFs and allow extraction and replacement of internal files?
Hacking Is there a Windows program for exploring RomFs?
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I don't know if there is one that will do exactly what you're asking, but you can always extract the romfs, change the files you need, and then rebuild it.
https://github.com/ihaveamac/3DS-rom-tools/wiki
https://github.com/ihaveamac/3DS-rom-tools/wiki
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