PackedScene Instantiate from Tool Script is preserving Signals when saved

[Jemy191]

Tested versions

• Reproductible in:
  v4.2.1.stable.mono.official [b09f793]
  Godot v4.1.3 stable mono
  Godot v4.1 stable mono

System information

Godot v4.2.1.stable.mono - Windows 10.0.19045 - Vulkan (Mobile) - dedicated NVIDIA GeForce RTX 3060 Ti (NVIDIA; 31.0.15.4592) - Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz (20 Threads)

Issue description

I'm experiencing unusual behaviour with tool script and packed scene instantiation.
When instantiating a PackedScene that has signals connection, the signals are saved to the scene file.
The nodes themselves saved, only the signals are.

Steps to reproduce

Download TestBugSignal.zip
1: open the project in either the mono version or the normal version.
2: open the scene Node2D(C#) or Test2(GDScript)
3: wait for the 10 number to print in the console
4: open the previously opened scene file in a text editor
5: notice the 10 signal connection in the file

Minimal reproduction project (MRP)

TestBugSignal.zip
or
Create a scene that as any signal connection in it.
Create a scene that as a script that has this code:

@tool
extends Node2D

@export var test: PackedScene:
	set(value):
		test = value
		refresh()

func _ready() -> void:
	refresh()

func refresh():
	if not test:
		return

	for i in 10:
		add_child(test.instantiate())
		print(str(i))

follow Steps to reproduce

[Rindbee]

Similar to #48064 and #85372.

[Jemy191]

@Rindbee yes thank it is the same bug

[rthomas-private]

I got this on v4.2.2.stable.official [15073af]
All Area2D body_entered() or body_exited() connections made through the editor using the node signals throw this error on scene load.
It happens when I reload a previously packedscene which I used to save the original scene.
Error stopped when I recreated all my Area2D connections in code using;
func _ready(): self.connect("body_entered", Callable(_on_body_entered))
and likewise for _on_body_exited
I notice it doesn't happen for area_entered, or indeed for any other signals I currently have.
hope this helps 🤷‍♂️