The sites are created during portal initialization, that is, when the server starts for the first time. So if you deploy your extension after that, your extension should trigger a re-initialization process, by setting the override value-param to true as said before:

<value-param>

    <name>override</name>

    <description></description>

    <value>true</value>

</value-param>

If this parameter is omitted, it is defaulted to false.

After your site is created, its preferences persists in database. When you modify your extension and redeploy it, you need to set importMode to either merge or overwrite to make your extension update/override the persistent data; otherwise, the modification will not take effect.

The valid options of importMode: