After Installing JLink 6.62 it offered a firmware update for the connected JLink. I performed the update (Firmware: J-Link OB-SAM3U128-V2-NordicSemi compiled Jan 21 2020 17:30:48) and now the JLink doesn't appear as a mass storage device. In Device Manager it says
This device cannot start. (Code 10) The I/O device is configured incorrectly or the configuration parameters to the driver are incorrect.
A device with an older firmware still works. Is there a way to reverse this firmware update? I've also emailed SEGGER about this issue but I'm not sure who is responsible.