I also had my files blown away on one HD and my SSD doesn't seem to work properly. I've tried moving the SSD around to other SATA slots and see if it is a cable or something else and it seems to work OK, but not in SATA 0.
One issue might be a coincidence, but both things happening at the same time is a bit much for me to believe. This is on an HP i7 Envy Phoenix desktop that was working fine until this upgrade. I do have these files backed up, but need to get a working system!
I had to boot off a windows to go USB to even start the diagnostic process from a GUI and I am still stumped as to what is going on.