### Godot version

Master (4.2)

### System information

Windows 11 - Vulkan - Nvidia RTX 4070 - intel i5 13600KF

### Issue description

As you can see in the video when you try to add multiple scenes in to the 3D viewport (only with multiple scenes) the editor throws this error.

```
ERROR: Can't add child '@Node3D@18837' to '@SubViewport@9274', already has a parent '@SubViewport@9274'.
   at: (scene\main\node.cpp:1411)
```


Video: https://youtu.be/BVcCIigQJDw

This happens in the latest master (pulled on 2.11.2023).

### Steps to reproduce

Drag couple of the 3d mesh scenes into the 3D viewport and then select multiple scenes and drag them over and observer the error.

### Minimal reproduction project

[TestSceneDragAndDrop.zip](https://github.com/godotengine/godot/files/13253741/TestSceneDragAndDrop.zip)

n.z = sqrt(max(0.0, 1.0 - dot(n.xy, n.xy)));
	COLOR.rgb = dot(n, sun_direction) * sun_color;
	COLOR.a = 1.0 - smoothstep(0.99, 1.0, length(n.xy));
}
)");
		sun_direction_material.instantiate();
		sun_direction_material->set_shader(sun_direction_shader);
		sun_direction_material->set_shader_parameter("sun_direction", Vector3(0, 0, 1));
		sun_direction_material->set_shader_parameter("sun_color", Vector3(1, 1, 1));
		sun_direction->set_material(sun_direction_material);
		HBoxContainer *sun_angle_hbox = memnew(HBoxContainer);
		VBoxContainer *sun_angle_altitude_vbox = memnew(VBoxContainer);
		Label *sun_angle_altitude_label = memnew(Label);
		sun_angle_altitude_label->set_text(TTR("Angular Altitude"));
		sun_angle_altitude_vbox->add_child(sun_angle_altitude_label);
		sun_angle_altitude = memnew(EditorSpinSlider);
		sun_angle_altitude->set_max(90);
		sun_angle_altitude->set_min(-90);
		sun_angle_altitude->set_step(0.1);
		sun_angle_altitude->connect("value_changed", callable_mp(this, &Node3DEditor::_sun_direction_angle_set).unbind(1));
		sun_angle_altitude_vbox->add_child(sun_angle_altitude);
		sun_angle_hbox->add_child(sun_angle_altitude_vbox);
		VBoxContainer *sun_angle_azimuth_vbox = memnew(VBoxContainer);
		sun_angle_azimuth_vbox->set_custom_minimum_size(Vector2(100, 0));
		Label *sun_angle_azimuth_label = memnew(Label);
		sun_angle_azimuth_label->set_text(TTR("Azimuth"));
		sun_angle_azimuth_vbox->add_child(sun_angle_azimuth_label);
		sun_angle_azimuth = memnew(EditorSpinSlider);
		sun_angle_azimuth->set_max(180);
		sun_angle_azimuth->set_min(-180);