Some meshes in scene file do not get updated when changing source file - other meshes do

### Tested versions

- Reproducable in Godot v4.3.stable.official [77dcf97d8]

### System information

Windows 11 - Godot v4.3.stable.official

### Issue description

Godot is not updating prefabs correctly.
The intended update architecture is:
.blend (raw meshes) -> .tscn (set up scene) -> .tscn (scene variant)

When editing a bodyshape of a 3d model the set up scene updates and SOME of the scene variants. Some just keep the old mesh shape.
I even tried to add a cube to the blendfile which appeared in ALL the scenes. The bodyshape however was still only updated in some scenes.

### Steps to reproduce

There are files for a giraffe and a racoon with different variants.
The racoon should have a clearer half-moon-shaped head.
The giraffe should have a thicker tongue.

The screenshot shows the folder structure and the variants that do get updated an the ones that don't.
Updating other objects like accessoires works however. It seems to be the body object only.


### Minimal reproduction project (MRP)

[prefab_bug_project.zip](https://github.com/user-attachments/files/17365371/prefab_bug_project.zip)

Open prefab_bug_project.zip in Godot v4.3 and reproduce the body-shape update with the supplied .blend, setup .tscn, and scene variants. Compare variants that update with those that retain the old body mesh, then trace the imported-scene or prefab dependency update path; done means all affected variants reflect the changed mesh while existing accessory updates still work.

Written by the indexing model from the issue text.