Godot version:
0afdc5c559520204987544d30560745dbf29a390
OS/device including version:
Windows 10, 64-bit, GTX 960
Issue description:
With an instance scene and "editable children" selected, add a Particles2D node to the child of that instance scene, and place it somewhere in the hierarchy, press F6 to scene preview. Then, switch to a different scene, then switch back and you will notice that Particles2D node is at the bottom.
This does not happen on 3.0.6
Example:

I did some more testing.
It actually moves to the bottom of the tree list, right when you scene preview (I checked remote tree). The mere act of scene switching doesn't cause this
Does it happen with other nodes?
@bojidar-bg Just tested it with Spatial, Control, Node2D, AnimPlayer, AudioStream, Timer, Tween, and CanvasLayer. Basically all of them so far
I've experienced this many times.
I've considered that Godot does not allow reorder the added node between children of instanced node.
It happens also with 2.x
So it happens with 2.x and the master branch, but did not happen with 3.0.6? That would be weird.
Or maybe it was fixed in 3.0 by those index="0" parameters that we eventually removed in most scenarios (#17562)? If so the bug should be reproducible in 3.1 alpha 2, but not 3.1 alpha 1.
to be more precise,
it can be moved between children node of instanced node in editor.
but it's moved to the bottom of instanced node when run, can be checked by remote inspector.
I believe this happens all version.
so I had workaround in _ready()
func _ready():
instanced_node.move_child(wanted_node, wanted_index)
Not critical for 3.1, kicking to 3.2. Sorry :(
Still valid in 3.2.2