### 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)

sun_environ_popup = memnew(PopupPanel);
		add_child(sun_environ_popup);
		HBoxContainer *sun_environ_hb = memnew(HBoxContainer);
		sun_environ_popup->add_child(sun_environ_hb);
		sun_vb = memnew(VBoxContainer);
		sun_environ_hb->add_child(sun_vb);
		sun_vb->set_custom_minimum_size(Size2(200 * EDSCALE, 0));
		sun_vb->hide();
		sun_title = memnew(Label);
		sun_title->set_theme_type_variation("HeaderSmall");
		sun_vb->add_child(sun_title);
		sun_title->set_text(TTR("Preview Sun"));
		sun_title->set_horizontal_alignment(HORIZONTAL_ALIGNMENT_CENTER);
		CenterContainer *sun_direction_center = memnew(CenterContainer);
		sun_direction = memnew(Control);
		sun_direction->set_custom_minimum_size(Size2(128, 128) * EDSCALE);
		sun_direction_center->add_child(sun_direction);
		sun_vb->add_margin_child(TTR("Sun Direction"), sun_direction_center);
		sun_direction->connect("gui_input", callable_mp(this, &Node3DEditor::_sun_direction_input));
		sun_direction->connect("draw", callable_mp(this, &Node3DEditor::_sun_direction_draw));
		sun_direction->set_default_cursor_shape(CURSOR_MOVE);
		sun_direction_shader.instantiate();
		sun_direction_shader->set_code(R"(
// 3D editor Preview Sun direction shader.
shader_type canvas_item;
uniform vec3 sun_direction;
uniform vec3 sun_color;
void fragment() {
	vec3 n;
	n.xy = UV * 2.0 - 1.0;