You can try the following method:
01. - Download the package in the attachments
02. - Decrypt your Rom with 3DS Lazy
03. - copy the decrypted "romfs" folder into the "RomFS Encrypt"-Folder from the attachments
04. - modify your "romfs"
05. - Run "
Use this to build a new RomFS.bat"
06. - you created a new romfs.bin
07. - Download and run Auto_CIA and decrypt your 3DS Rom
08. - copy your fresh-builded romfs.bin into the tmp-folder of Auto_CIA (after decrypting rom)
09. - rebuild your 3DS Rom with Auto_CIA
10. - You created a new .cia file (or 3ds) with your modified and rebuilded romfs.bin!
This worked well for me ,you can check my modified "Harvest Moon - A New Beginning" here:
Rar Archive
https://anonfiles.com/file/5ec1deeb75eb6671ca2cd97abe34b439