i had the same issue of only the one xci file show up that was on the flash drive and my switch crashed when switching to the install menu to install a nsp. I didn't even start the install before the switch crashed. i was using a cheap sandisk flash drive. when using a higher quality sandisk...
from my personal experience, Nintendo doesn't attempt to fix anything. I had to send my switch in for repair because i used the NYKO dock, i received a completely new switch with a different serial number less than a week after i sent it in even though i was quoted 2-3 weeks for a repair.