Obviously, you are deploying the configuration file because after restarting IIS an updated configuration is available.
It looks like you are using an external file for your AppSettings:
<appSettings file="my-app-settings.config" />
This is useful for keeping web.config clean, especially if you support different configuration files for a separate environment (for example, dev, testing, prod). However, the catch of this approach is that ASP.NET does not automatically detect changes to the external file, so your settings are not updated automatically.
Per MSDN , changes to the .NET Framework 2.0 in a separate file do not restart subsequent applications. It looks like your solution would be to not use an external file in this scenario.
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