USBLoaderGX deletes nincfg.bin from both SD and USB before launching nintendont, because users requested it (they incorrectly thought it was what made nintendont crash, but whatever I did it to please everyone)
If you use an old version of nintendont or if you don't use autoboot, it re-creates the nincfg.bin in both loader partition+game partition.
if you use a autoboot and the new nintendont versions with arguments support, it doesn't create the nincfg.bin file at all and every settings are passed by arguments in memory at nintendont launch.
If users need an option to always write/keep the nincfg.bin to launch nintendont from HBC with the same settings than the previous launch from USBGX, I can add it.