Repository: godot
Issue: Renaming a folder with a `.glb` file, still shows an empty folder with the old name.
Labels: bug,topic:import,topic:3d

### Godot version

v3.5.beta1.official [b9b23d222], v3.4.2.stable.official [45eaa2daf]

### System information

Windows 10 21H1

### Issue description

Renaming a folder with a `.glb` file, still shows an empty folder with the old name.

### Steps to reproduce

Setup:
- Open the attached project: [issue_rename_folder_with_glb_file.zip](https://github.com/godotengine/godot/files/7936710/issue_rename_folder_with_glb_file.zip)
- Or create a new Godot project,
create a new folder: `a`
and add a `.glb` file into the new folder

The attached project has a folder named: `a`
that includes the file: `fantasy-town-kit-1.0\Models\GLTF format\bannerGreen.glb`
from the asset pack: https://www.kenney.nl/assets/fantasy-town-kit

When the `.glb` file has been imported,
then the `a` folder contains the files:
```
bannerGreen.glb
roof.material
roofLight.material
wood.material
```

Steps:
- In the FileSystem dock
- Select the folder `a`
- Rename it `F2` or `Right click > Rename...`
- Type: `b`
- Press `enter` or mouse click on the `Rename` button, confirm the new name

### Observed
The FileSystem dock shows two directories:
```
 a
>b
```
The `b` has an arrow to the left of the folder icon,
it indicates that the folder contains some files,
clicking on the arrow unfolds the files:
```
bannerGreen.glb
roof.material
roofLight.material
wood.material
```

### Expected
The folder with the old name shouldn't remain visible.


### Possible cause
When the folder is renamed, then the system console shows the messages:
>ERROR: Can't find file 'res://a/roof.material'.
   at: (editor/editor_file_system.cpp:1668)
ERROR: Can't find file 'res://a/wood.material'.
   at: (editor/editor_file_system.cpp:1668)
ERROR: Can't find file 'res://a/roofLight.material'.
   at: (editor/editor_file_system.cpp:1668)

Maybe the errors stop Godot, before the FileSystem dock is refreshed.

### Notes
It seems to be a refresh issue.

Because the old folder disappears:
- In the Windows File Explorer, as soon as the folder is renamed.
- A new folder is added to the FileSystem dock

And when one attempts to delete the folder with old name.
Then a `Load Errors` window opens, with the message:
```
Cannot remove:
res://a/
```

### Question
In `v3.4.2.stable.official [45eaa2daf]`, the system console can be toggled with: `Editor > Toggle System Console`
But in `v3.5.beta1.official [b9b23d222]` that option is missing from the Editor menu.

![Godot_v3 5-beta1_win64_3U7KmqSbEP](https://user-images.githubusercontent.com/13420573/151052354-e3be326a-3bd8-414f-ad04-431bdc5158a1.png)

I got the System Console messages in `3.5.beta1` by starting: `.\Godot_v3.5-beta1_win64.exe`
from a Windows PowerShell prompt.

Is the missing menu option a `beta` issue?
Or is it being removed in future versions?

It seems like it could be useful for finding the possible cause for an issue, as described above.


### Minimal reproduction project

[issue_rename_folder_with_glb_file.zip](https://github.com/godotengine/godot/files/7936710/issue_rename_folder_with_glb_file.zip)