The problem happens when the application uses both IMenuBuilder.HideBuiltInMenuItem() and ContextService.Subscribe(), as shown below.

        public MainControl(IAppHost appHost)
            : this()
        {
            AppHost = appHost;
            AppHost.Closing += AppHostOnClosing;

            //1. Add custom menu and hide 
            AppHost.Menu.OnDisplayContextMenu(builder =>
            {              
                var openAppMenuItem = new UserMenuItem("Test");
                openAppMenuItem.IsEnabled = true;
                builder.AppendCustomMenuItem(openAppMenuItem);            
                foreach (BuiltInCommand cmd in System.Enum.GetValues(typeof(BuiltInCommand)))
                {
                    builder.HideBuiltInMenuItem(cmd);
                }
            }
           );
            //2. Subscribe to context
            AppHost.ContextService.Subscribe(ctx =>
            {
            }
           );
           
        }

The Related, Trading and Send To commands appear upon right-click. These commands appear disabled, but not hidden.

However, after removing ContextService.Subscribe() part, the built-in menu items are completely hidden.

        public MainControl(IAppHost appHost)
            : this()
        {
            AppHost = appHost;
            AppHost.Closing += AppHostOnClosing;
            //1. Add custom menu and hide 
            AppHost.Menu.OnDisplayContextMenu(builder =>
            {              
                var openAppMenuItem = new UserMenuItem("Test");
                openAppMenuItem.IsEnabled = true;


                builder.AppendCustomMenuItem(openAppMenuItem);             
                foreach (BuiltInCommand cmd in System.Enum.GetValues(typeof(BuiltInCommand)))
                {
                    builder.HideBuiltInMenuItem(cmd);
                }
            }
           );           
        }

I will contact the Eikon team to verify this issue.

As far as I remember, preventing an App to completely redefine Eikon right-click was a design choice (Product), to enforce look and feel consistency. Dev team and product should be involved here.

Your code works fine in my environment. After hiding all built-in menu items, I can see only my custom menu after right click.

You may need to verify the version of Integration API and Eikon. I am using ThomsonReuters.Eikon.Integration.1.2.13.6440 and Eikon 4.0.37555.