update app.config file programmatically with
Configuration config = ConfigurationManager.OpenExeConfiguration(ConfigurationUserLevel.None);
You can use the following code:
private void UpdateConfig(string key, string value, string fileName)
{
var configFile = ConfigurationManager.OpenExeConfiguration(fileName);
configFile.AppSettings.Settings[key].Value = value;
configFile.Save();
}
Where: fileName is the full path + application name (c:\project\application.exe)
In your case, change the AppSetting by Sections:
configFile.Sections["nhibernateSettings"]