The .app file type from around 2010 of the 3DS's development does not work with ctrtool since it is made for a prototype firmware and many differences between .app formats, you can find every prototype 2010 3DS E3 .app files here with everything else: https://archive.org/details/3ds-prototype-emunand-setup-kit
The .app file type from around 2010 of the 3DS's development does not work with ctrtool since it is made for a prototype firmware and many differences between .app formats, you can find every prototype 2010 3DS E3 .app files here with everything else: https://archive.org/details/3ds-prototype-emunand-setup-kit