Unable to reload project with save after changing resource script

### Tested versions

4.3 stable, 4.4 beta1

### System information

Godot v4.3.stable - Windows 10.0.19045 - GLES3 (Compatibility) - Radeon RX 560 Series (Advanced Micro Devices, Inc.; 31.0.14001.45012) - Intel(R) Core(TM) i5-4570 CPU @ 3.20GHz (4 Threads)

### Issue description

After changing the custom resource script, it is impossible to reload the project, saving it, the pop-up selection window appears even after selection.

https://github.com/user-attachments/assets/5c17a701-a523-4b5a-9619-1874d1f71f2b

### Steps to reproduce

1. Open MRP
2. Open the resource `new_resource.tres` and open its script
3. Edit the resource script
4. Reload the project using `Project->Reload Current Project`
5. The pop-up window will appear again.

### Minimal reproduction project (MRP)

[bug.zip](https://github.com/user-attachments/files/18540803/bug.zip)

Start with the attached bug.zip minimal reproduction project and reproduce the failure by editing new_resource.tres's custom resource script, then choosing Project → Reload Current Project. Trace the reload and save prompts involved in this scenario; done means the project reloads once without repeatedly showing the pop-up after the selection is made.

Written by the indexing model from the issue text.