I can’t prove this without logs from the Roon core system, but I think it’s very likely that the problem here is that both USB drives have the same NTFS “Volume ID”, and Roon gets confused as you’ve seen. If you upload logs I can confirm, or you can try the fix blind:
You need to change the Volume ID of one of the two disappearing drives. To do this,
- Download the VolumeID program here: https://technet.microsoft.com/en-us/sysinternals/bb897436.aspx
- Follow the instructions here: http://www.wintips.org/how-to-change-hard-disks-volume-serial-number-volume-id/
(For reference, this is the first thing I’d expect given “Roon only sees one of two drives” and, importantly, “both drives are the same model/size/etc USB from the same vendor”)