I have thought of something else. When I did the remote upgrade, I picked the generic host install msi file that I downloaded from the Beta page. Could that be the reason for the settings to be erased - because I didn't customize the msi installer first?
Certainly, not. Quite the contrary - if you use the "vanilla" Host during upgrade, the Host settings should be intact.
I assumed that the upgrade would re-use the existing config from the Host I was upgrading.