If you had bothered to read https://github.com/d0k3/GodMode9 and https://wiki.hacks.guide/wiki/3DS:Dump_system_files already, you would see that those files are only there when you run Godmode9 from boot9strap. That's just how it is.
My sd card is not working anymore, I bought another of 64GB, but I cannot dump the file because it is not in memory virtual, even boot11.bin is not there, do I need to fix my nand or something?
I need all this because I want to use it with custom...