I got the bike back today from the dealer. The situation is much less dire than I had understood it to be. Unfortunately, all the information I have about the incident is third hand, but I think I have a better understanding of it now.
Since I got home without incident, the problem that stranded me after the firmware update seems to have been fixed when the battery management board was replaced.
The state of the "bad" battery as I understand it from the dealer is that it is charging, but that the bike cannot balance the two batteries with each other because the "bad" battery is so much weaker than the "good" battery. Apparently Zero told the dealer that the "bad" battery had been degrading for a while (as determined from the logs). The dealer indicated that the bike may be able to get some use out of the "bad" battery, but he did not know how much.
Tracking the battery usage on the way home from the dealer seems to indicate that the battery behavior is roughly comparable to the behavior before the firmware update.
The dealer also said that they had spent upwards of twenty hours with Zero working this all through. I did not owe the dealer anything when I picked up the bike. Hopefully the dealer is being reimbursed for their time.
To their credit, Zero did spend a lot of effort on this and it looks like the bike was returned in roughly the condition I left it in. They paid to have the battery management board replaced, which fixed the problem that stranded me. In the end, the "bad" battery was not "destroyed", but just weak.