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I don't have any program to suggest.
I'd just recommend that you don't mess with the ISO (don't convert, align, shrink, discex, or whatever).
just use the raw copy, it will rename the filename and folder, that's all.
You can rename manually if you want.
game.iso and disc2.iso
you can put in any sub-folder name you want, it's just quicker for USBLoaderGX if you provide the titleID. if you don't, the loader will open the ISO to extract the ID from it.
the loader will work with all these folder and file names :
https://gbatemp.net/threads/usb-loader-gx.149922/page-848#post-4628403
I'd just recommend that you don't mess with the ISO (don't convert, align, shrink, discex, or whatever).
just use the raw copy, it will rename the filename and folder, that's all.
You can rename manually if you want.
game.iso and disc2.iso
you can put in any sub-folder name you want, it's just quicker for USBLoaderGX if you provide the titleID. if you don't, the loader will open the ISO to extract the ID from it.
the loader will work with all these folder and file names :
https://gbatemp.net/threads/usb-loader-gx.149922/page-848#post-4628403