GDScript subresources do not save correctly when owner is custom resource

[Benpaste]

Tested versions

• Reproducible in 4.2.1.stable

System information

Godot v4.2.1.stable - Windows 10.0.19045 - Vulkan (Forward+) - dedicated AMD Radeon RX 5700 (Advanced Micro Devices, Inc.; 31.0.24002.92) - AMD Ryzen 5 3600 6-Core Processor (12 Threads)

Issue description

When a custom Resource contains an exported GDScript, many of the ordinary methods for saving edits to that script file stop working.

WHAT DOES NOT WORK:

• Ctrl + S
• Ctrl + Alt + S (save script)
• Shift + Alt + S (save all)
• right-clicking on the script in the Scripts Panel and clicking "Save"
• clicking "Save" on the dropdown for the exported GDScript, in the parent resource's Inspector window.
• Running the project
• Quitting the project - this results in a "Save changes before quitting?" dialogue that reappears every time you press "Save & Quit"

WHAT DOES WORK:

• Closing the script from the Scripts Panel (prompts a "Close and save changes?" dialogue). Works ONCE and will not save further edits.
• Clicking "Save" on the parent resource in the Inspector.

Steps to reproduce

1. Create a new GDScript file, resource_class.gd.

extends Resource
class_name CustomResource
@export var custom_script: GDScript

2. Create a new instance of this resource, resource_instance.tres.
3. Navigate to resource_instance.tres's Inspector tab, click on Custom Script and click New GDScript.
4. Type "Hello World" in the new Custom Script. Press Ctrl+S to save.
5. Observe that the exported script's name in the Scripts Panel changes from [unsaved](*) to new_resource.tres::GDScript_xxxxx(*).
6. Observe that pressing Ctrl+S does not save any changes to the Custom Script. Opening resource_instance.tres in a text editor will confirm that no changes are being saved.

Minimal reproduction project (MRP)

Export Script Saving MRP.zip

[KoBeWi]

Looks like duplicate of #86696?

[Benpaste]

It is, thank you. Wasn't able to find it via search but that describes my problem exactly

[akien-mga]

Consolidating in #86696.