USB ports no longer work after update

[Jaclyn]

Before I get into the issue, I would like to post two small disclaimers. 1: I am trying to help my brother with this issue via proxy so the amount of information I can get is rather limited. 2: This is mainly just an academic issue as I told him the easiest way of solving it since I was not there was to wipe the SD card and do a fresh install of RetroPie so unless the issue gets replicated, it should be solved.

Pi Model: 3
RetroPie Version Used: I assume 4.1 since the issue occurred after her updated
Built From: pre-made SD.
USB Devices connected: Cell phone in tether mode to update.
Controller used: none
Error messages received: none

So my brother used his cellphone in tethering mode via USB to update his raspberri pi and afterwards none of the USB port detected when anything was plugged in. I believe he was trying to update the retropie software, but I can't say for certain because I wasn't there; he may have been trying to update some other software on the raspberry pi. He got his SD card with retropie installed so I don't know what other software he would be trying to update of not the retropie software. The USB ports still supply power, but the system is not recognizing any input from any device plugged into the ports. Unfortunately, that's all the information I could gather from him, so if you know what might have gone wrong, I'd love to hear it.