Sounds like he updated with conjournx (or how ever you spell it) with the exfat update but never put the sd card in and got the small exfat update from Nintendo officially so nintendo doesn't have the console as registered to having the update so didbt give him the exfat part when the kid updated.
So to fix this, get a fat32 sd card (dobt recommand the one you normally use as you will loose all the data), set it up to boot atmosphere and the 10.4 update files and reflash the update with the exfat option
Or just download the update when in the os and connect to Nintendo servers for the small patch. If your kid updated nintendo already has the logs and if you have nsps installed you might be already flaged for a ban