No that's fine. Just continue from that point. The same happened to me and it still worked.Just ran into a problem. When I typed the command "ctrtool -p --exefs=exefs.bin --romfs=romfs.bin FILENAME.cxi" replacing FILENAME With the name of my .CXI file, it left me with an error message:
"Error, exheader hash mismatch. Wrong key?"
Am I doing anything wrong?