Merging instanced node from another scene bug

[SoulForMachine]

Godot version:
v3.1.1.stable.official
v3.2.dev.custom_build.e71cf83f

OS/device including version:
All

Issue description:
When using Merge From Scene, and then selecting a node in another scene that is an instantiation of a third scene, and then checking Editable Children on the merged node, all children of that node will be duplicated.

Steps to reproduce:

• Create a scene, add root Node2D, name it Scene1, add a Sprite node as child. Save as Scene1.tscn.
• Create a scene, add root Node2D, name it Scene2, instantiate Scene1.tscn as child. Save as Scene2.tscn.
• Create a scene, add root Node2D, name it Scene3.
• On root node Scene3, right-click and use Merge From Scene, select Scene2.tscn, select Scene1 node.
• On newly merged node, right-click and check Editable Children.
• Select the grayed Sprite node move it a little bit.
• Save the scene as Scene3.tscn and run it.
• The scene in game has 2 sprites displayed.
• Close the game and close the Scene3.tscn tab in editor.
• Reopen Scene3.tscn again. Now 2 Sprite nodes are visible in editor too, one is grayed and one isn't. When one is selected the other is automatically selected too.

Minimal reproduction project:
MergeInstanceTest.zip

[SoulForMachine]

I think I found out what the problem is. EditorSubScene, from which a sub-tree is selected to merge, did not instance the source scene with PackedScene::GEN_EDIT_STATE_INSTANCE, so if the node we are merging is in fact an instanced scene in the source scene, it won't have its data.instance_state set. Later, when Editable Children is checked for the merged node and the scene is saved, SceneState::_parse_node will treat child Sprite of the merged node as not being part of the instanced scene and will write it into the tscn.

[gd_scene load_steps=3 format=2]

[ext_resource path="res://Scene1.tscn" type="PackedScene" id=1]
[ext_resource path="res://icon.png" type="Texture" id=2]

[node name="Scene3" type="Node2D"]

[node name="Scene1" parent="." instance=ExtResource( 1 )]

[node name="Sprite" type="Sprite" parent="Scene1"]
position = Vector2( 160, 31 )
texture = ExtResource( 2 )

[editable path="Scene1"] 

So the sprite is duplicated. I changed the scene instantiation call in EditorSubScene::_path_changed to:
scene = ps->instance(PackedScene::GEN_EDIT_STATE_INSTANCE);

This fixes the problem, but some more feedback would be helpful since I'm new to Godot. I see that @reduz and @akien-mga touched most of this function, so please advise if this is correct solution.

[KoBeWi]

Still valid in ee36e08

[akien-mga]

Fixed by #34892 and #45943.