Files have been modified outside of Godot. When linked Control to Node2d

Godot Version

4.4.stable

Question

I am having a strange issue with the editor, I have linked the Control which is a scene of dialogue manager, to the one of the levels ( Node2d ), and now every time when I run the game and close it, Godot shows the message that the Node2d root .gd script has been modified, has anyone encountered such issue?
Just double checked, it is clearly related to the Control node being added to Node2d, tried deleting it, and the issue does not reproduce

I have restarted Godot and re-added the Control node, now everything works correctly, I did this 3 times, and it “fixed” itself on 3rd. 3rd time’s the charm

Reason This issue beginned from where I’m tried change with function “editable child” new inherit .tscn file which connected with .glb or .blend files.
I attached this .tscn to another object like child and changed him with function “editable child”

Solving problem: after making .tscn from .glb or .blend file. This .tscn need open with right button of mouse and choose “New inherit scene” again, then save this with another name or add number 2 to name and save like another file .tscn. Now attach this .tscn to another object like child , choose “editable child” with right button. And use it like how you want!