Partitioning secondary internal hard drive failure

So the problem was with the cable. Apparently one of the small pins on the cable that connected the optical drive to the motherboard, got broken.

If it was a total failure of the drive this may have been more obvious, alas, it was not. It merely caused the drive to work in an unstable manner.

As soon as I replaced the flex-cable with a salvaged one, the problem disappeared.

I’m afraid your hard drive is dying. Updating can be somehow hard drive intensive, so it’s not that surprising that it died during an update. If you have no backup, copy your important data to another hard drive with another computer¹.

You can still try to save it with utilities such as DiskWarrior.

Otherwise, you’ll have to buy a new hard drive and install it in your Mac Pro, then copy your data back to it.

1. And start doing regular back up right now.