I have a config file app.exe.config and appSettings section has something like this:
using an external config file is transparent for the application,
this part is o.k
and also this:
change your code to be like this:
Configuration config = ConfigurationManager.OpenExeConfiguration(Application.ExecutablePath);
config.AppSettings.Settings["var1"].Value = "value 11";
config.Save(ConfigurationSaveMode.Modified);
ConfigurationManager.RefreshSection("appSettings");
referring an external configuration file is transparent to the application, so you don't have to call it directly. you can use the default appSetting section in the configuration manager.
Good luck