Write appSettings in external file

using an external config file is transparent for the application,

this part is o.k

</configuration>
    <appSettings configSource="app.file.config" />
</configuration>

and also this:

<?xml version="1.0" encoding="utf-8" ?>

<appSettings>
  <add key="var1" value="value 1" />
  <add key="var2" value="value 2" />
  <add key="var3" value="value 3" />
</appSettings>

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

A more complete answer to prevent confusion:

Setup:

1. Commandline project called 'app'

2. app.exe.config file, App.config:

   <appSettings file="App.Settings.config"></appSettings>
   

3. App.Settings.config file with 'Copy to Output Directory'= 'Copy Always'

   <?xml version="1.0" encoding="utf-8"?>
   <appSettings>
     <add key="test" value="OVERRIDDEN"/>
   </appSettings>
   

4. Program.cs:

   static void Main(string[] args)
   {
       try
       {
           Console.WriteLine("Local Config sections");
           var exepath = (new Uri(System.Reflection.Assembly.GetExecutingAssembly().CodeBase)).LocalPath;
           Configuration config = ConfigurationManager.OpenExeConfiguration(exepath);
   
           config.AppSettings.SectionInformation.ConfigSource = "App.Settings.config";
   
           Console.WriteLine("BEFORE[test]=" + config.AppSettings.Settings["test"].Value);
           Console.WriteLine($"BEFORE[testExternalOnly]={config.AppSettings.Settings["testExternalOnly"]?.Value}");
   
           //to avoid: Error CS0266
           //Explicitly cast 'System.Configuration.AppSettingsSection'
           AppSettingsSection myAppSettings = (AppSettingsSection)config.GetSection("appSettings");
   
           myAppSettings.Settings["test"].Value = "NEW";
           if (!myAppSettings.Settings.AllKeys.Contains("testExternalOnly"))
               myAppSettings.Settings.Add("testExternalOnly", "NEWEXTERNAL");
   
           config.Save(ConfigurationSaveMode.Modified);
           ConfigurationManager.RefreshSection("appSettings");
   
           //Read updated config
           Console.WriteLine("AFTER[test]=" + config.AppSettings.Settings["test"].Value);
           Console.WriteLine("AFTER[testExternalOnly]=" + config.AppSettings.Settings["testExternalOnly"].Value);
   
           Console.WriteLine("AFTER CONFIG EXTERNAL FILE: " + System.IO.File.ReadAllText("App.Settings.config"));
   
           Console.WriteLine("AFTER CONFIG FILE: " + System.IO.File.ReadAllText(System.AppDomain.CurrentDomain.FriendlyName + ".config"));
   
   
           //Shut current config
           config = null;
   
           //Open config
           config = ConfigurationManager.OpenExeConfiguration(exepath);
           config.AppSettings.SectionInformation.ConfigSource = "App.Settings.config";
   
           Console.WriteLine("AFTER[test]=" + config.AppSettings.Settings["test"].Value);
           Console.WriteLine("AFTER[testExternalOnly]=" + config.AppSettings.Settings["testExternalOnly"].Value);
   
           Console.WriteLine("AFTER CONFIG EXTERNAL FILE: " + System.IO.File.ReadAllText("App.Settings.config"));
   
           Console.WriteLine("AFTER CONFIG FILE: " + System.IO.File.ReadAllText(System.AppDomain.CurrentDomain.FriendlyName + ".config"));
       }
       catch (Exception ex)
       {
           Console.WriteLine(ex.Message);
       }
       Console.WriteLine("press the ENTER key to end");
       Console.ReadLine();
   
   }
   

This will result in App.Settings.config file updated to be on the filesystem as:

<?xml version="1.0" encoding="utf-8"?>
<appSettings>
  <add key="test" value="NEW" />
  <add key="testExternalOnly" value="NEWEXTERNAL" />
</appSettings>