Moving A Script That Extends Resources Lead To Missing Dependecy

### Tested versions

Reproducible in 4.2.2

### System information

Windows 11, Godot v4.2.2 Forward Renderer

### Issue description

When moving a folder or a script that extends Resources, it could result in missing dependencies.

### Steps to reproduce

I was able to reproduced this issue using my dialogue system, which relies on resources. Based on the reproduction project, follow these steps:

1. Open the project.
2. Move the dialogue_res_scripts folder to a different location (e.g., dialogue_resources folder).
3. Reload the project.

Video Guide

https://github.com/godotengine/godot/assets/45304248/91c54af3-6a5a-4d39-91d7-ad1f88aaf180

### Minimal reproduction project (MRP)

[ResMissingDependecy.zip](https://github.com/user-attachments/files/15830627/ResMissingDependecy.zip)

Open the attached ResMissingDependecy.zip in Godot 4.2.2 and reproduce the problem by moving the dialogue_res_scripts folder, then reloading the project. Trace the resource dependency handling involved; done means moving the folder no longer leaves missing dependencies after reload. No source file or test is identified in the issue.

Written by the indexing model from the issue text.