Xavier H01 Kit USB Does Not Work after apt update and flashing

After using sudo apt update on the unit the USB ports stopped working. As I understand, the drivers that were with the device only worked with the shipped version of the OS, 4.6.1.

I was unable to SSH into the device due to it not being enabled and was forced to flash it with 4.6.1 using the Seeed Wiki article. The flash seemingly worked as I am seeing a screen asking to accept the ToC for the L4T End User Agreement, however, the USB ports are still not working and I still cannot SSH into the root user on my local network.

What else can be done to get the USB ports working once again?

EDIT: I have not tried the SDKmanager from Nvidia but will do so now.

EDIT 2: I walked away for a moment and was met with the flash being incomplete for some reason, so SDK manager did not work. Probably worth another attempt but will wait for someone to post here.

Bumping for visibility.