This is all occurring on my local test environment.
My EE 1.6.6 installation had MSM turned on, but only one site of the three set up in MSM was in use, which was site_id 2.
I successfully ran the updater from version 1.6.6 to version 2.1.3, but upon first access to the CP I get the error:
Site Error: Unable to Load Site Preferences; No Preferences Found
I did copy the EE 2.x MSM files to the required places in the new EE 2 install location. I have also tried setting multiple_sites_enabled to “n” in config.php, but this has no effect.
I traced this error to system/expressionengine/core/EE_Config.php. It’s checking the value of exp_sites:site_system_preferences, and it’s not what was expected.
After the update, the content of site_system_preferences of each of the three rows in exp_sites is just ‘czowOiIiOw==’.
In the exp_sites table on the original live 1.6.6 site, the site_system_preferences field is filled in with a large serialized php array.
So it looks like this setting is not getting carried over properly through the update?