### 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)

Ref<SurfaceTool> st = memnew(SurfaceTool);
	Ref<SurfaceTool> st_xray = memnew(SurfaceTool);
	st->begin(Mesh::PRIMITIVE_LINES);
	st_xray->begin(Mesh::PRIMITIVE_LINES);
	for (int i = 0; i < 12; i++) {
		Vector3 a, b;
		aabb.get_edge(i, a, b);
		st->add_vertex(a);
		st->add_vertex(b);
		st_xray->add_vertex(a);
		st_xray->add_vertex(b);
	}
	Ref<StandardMaterial3D> mat = memnew(StandardMaterial3D);
	mat->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
	mat->set_flag(StandardMaterial3D::FLAG_DISABLE_FOG, true);
	const Color selection_box_color = EDITOR_GET("editors/3d/selection_box_color");
	mat->set_albedo(selection_box_color);
	mat->set_transparency(StandardMaterial3D::TRANSPARENCY_ALPHA);
	st->set_material(mat);
	selection_box = st->commit();
	Ref<StandardMaterial3D> mat_xray = memnew(StandardMaterial3D);
	mat_xray->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
	mat_xray->set_flag(StandardMaterial3D::FLAG_DISABLE_FOG, true);
	mat_xray->set_flag(StandardMaterial3D::FLAG_DISABLE_DEPTH_TEST, true);
	mat_xray->set_albedo(selection_box_color * Color(1, 1, 1, 0.15));
	mat_xray->set_transparency(StandardMaterial3D::TRANSPARENCY_ALPHA);
	st_xray->set_material(mat_xray);
	selection_box_xray = st_xray->commit();
}
Dictionary Node3DEditor::get_state() const {