In my Azure App Service I want to update application settings, but after publish from VS the keys doesn't override values from local Web.config
In the result my web.config on azure contains values from local settings
<connectionStrings>
<add name="MainConnectionString" connectionString="ConnectionStringToReplaceByAzure" providerName="System.Data.SqlClient" />
</connectionStrings>
<appSettings>
<add key="MS_SigningKey" value="Overridden by portal settings" />
</appSettings>
Azure never physically modifies your web.config file. Instead, the Azure App Setting is injected into the config system at runtime. So even though you don't see it in web.config, if you query it from your app you will get the correct value.