Situation: 1.9 site installed and registered
Upgrade to 2.1 in different URL

1) Going to register against Mooch, it seems to be a new registration, all the 1.9 preferences lost.
2) I guess this will lead to duplicate site registration where the site is the same.
3) Registered under 2.1, the site does not show in listing immediately
4) Tried to update 2.1 registration, got: An error occurred during registration, please try again later. (Invalid external api parameter: moodleversion (Invalid external api parameter))
5) Tried to take a look to the "manage registrations" interface. It has been amortized (Aug 22th).

And that's my experience. Feel free to extract conclusions