Scene state is missing value after property passed to local_to_scene ShaderMaterial

### Tested versions

v4.2.2.stable.official [15073afe3]
v4.3.rc3.official [03afb92ef]

### System information

Ubuntu

### Issue description

This is not super straight forward to explain so I'll have to rely on the MRP.

In essence, I do this:
```gdscript
var packed_scene = preload("res://entity.tscn")
print(packed_scene.get_state().get_node_property_value(0, 2))
```
prints:
```
[1, 2, 3]
```

Then a moment later that code is ran again, but prints:
```
[]
```

### Steps to reproduce

Here's what happens in the MRP:

1. We preload a `tscn` file.
2. The `tscn` file contains a node with an array property `my_prop` and a serialized value: `my_prop = Array[int]([1, 2, 3])`
3. We instantiate from the packed scene, add the resulting node instance to the tree, and pass the aforementioned property into `material.set_shader_parameter()` where `material` is a `ShaderMaterial` that has `local_to_scene` set to `true`.
4. We reload the current scene, bringing us back to step 1. again, only this time the packed scene state is faulty: the value of my `my_prop` is an empty array.

### Minimal reproduction project (MRP)

[godot_4_packed_scene_values_missing_bug.zip](https://github.com/user-attachments/files/16571127/godot_4_packed_scene_values_missing_bug.zip)

Start with the attached minimal reproduction project and trace the packed scene state across the reload after the ShaderMaterial with local_to_scene enabled receives the array through set_shader_parameter(). Verify the behavior using get_node_property_value(0, 2); done means the serialized my_prop value remains [1, 2, 3] rather than becoming an empty array.

Written by the indexing model from the issue text.