Qlik GeoAnalytics have a few components and the upgrade for each is slightly different:
1. GeoAnalytics Server:
You can run the new installer directly to upgrade and all the settings remains. Please see Installing Qlik GeoAnalytics server
"To upgrade a GeoAnalytics server to the latest version, run the latest version of the installer. Configurations from the previous installation will be loaded (including data package services)."
You can also refer to Qlik GeoAnalytics Server Installation Guide
2. Qlik Geo analytics Data Package
There is no document so far stating that data package must be upgraded to match the server version. However it is recommended to upgrade to the later version of data package as it will provide latest data.
You can refer to upgrade section on the installation guide from the download site:
See section "10. Upgrading the map data"
Qlik GeoAnalytics Data Package Installation Guide
3. Qlik Geo Connector
You can run the installer directly to upgrade the connector. Once it finishes, you need to license it again.
Qlik Fix: Installing GeoAnalytics Connector with Qlik Sense
The activation part is the same as the new install.
4. Qlik Geo analytics extensions
To upgrade the extensions you have to remove the existing ones first otherwise the extension with the same name is detected.
You can keep all the GeoAnalytics virtualization there. But as the core for these extensions are change, you need to remove and re-create the GeoAnalytics virtualization for any fix or improvement in new extension.