I'm still trying to understand why my 6TB USB HDD became corrupted twice. I think the first time was because I hadn't powered up the drive before turning the Pi on. I have a theory that the second time could have been caused by the Pi trying to boot from the 6TB HDD rather than the 128GB SSD even though the 6TB drive was powered up.
I don't think its going to be possible (tried googling but haven't found anything to support the idea) but I'd like to be able to say to the Pi - "you can boot from the SSD but not the HDD" by USB port, disk name or anything. Is there a way?