Your run time configuration settings like that won't persist as that Config Repository is only loading the config into memory and doesn't deal with persistence, so you are only setting an element in memory when you set a config value. That memory is gone after the request is finished; every request is starting a new process that is booting the framework fresh and loading the configuration.
You should probably look into storing your settings in the database and caching them. Then you could retrieve them from your persistent storage and then set those configuration values based on what you pulled for your settings (at run time).
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