Instead of using the standard Logout activity from the toolbox, you should use the Sign Out / Reset App action that is designed specifically for Native Mobile apps. The default Logout action is meant for web behavior and can cause restart messages in native apps.
First, make sure the Native Mobile Resources module is installed and up to date in your project. Then open your nanoflow (or the microflow it calls) and remove the default Logout activity. Search for the JavaScript action called SignOut (or Sign_Out) and use that instead.
This action clears the authentication tokens stored on the device and reloads the native client internally. As a result, the app returns cleanly to the login screen without showing the restart error message.
This is my nanoflow