I had an issue where on rebooting the mac it said I was missing a disk. I know this has something to do with the Thunderbolt controller not starting correctly. After shutting everything down and rebooting it was fine it just took a couple of minutes to rebuild the missing disk, it's still a scary thing to see. Is there any way to prevent this error on a reboot, should I always completely switch off the Thunderbay before a reboot or is this issue being worked on? Thanks!
If only one disk is missing, this means the disk was hanging. Perhaps if you looked at the enclosure, one disk light was solid on.
I would put a SoftRAID disk label on that disk. See if it happens again. If it does, swap the disk to another slot, and see if the hang follows the disk or the slot. then you have a clue which is failing.

