I think that the problem is due to a virus that attacks the boot sector
An unconfigured/unformatted mass storage device would still show up in the device tree of the system control manager, or at
least as an unknown USB device. Did you check?
If the boot sector sector is damaged, the device would be accessible by data rescue tools.
I also once experienced a case, where an USB memory stick lost it's identity, but showed up as a different mass storage
device (apparently the controller chip's default type) afterwards. That's why I guessed, that the identity (the USB
descriptor table) is stored in a flash memory.
Even if the device isn't identifying as a mass storage device, it should take part in USB device enumeration and be visible
to software tools. Or it's completely dead, but then it's most likely a hardware problem.