Metadata is being overwritten on first time opening a project

### Tested versions

4.5stable (but was happening before)

### System information

Godot v4.5.stable - Windows 11 (build 26100) - Multi-window, 1 monitor - Vulkan (Forward+) - dedicated NVIDIA GeForce RTX 2060 (NVIDIA; 32.0.15.7703) - Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz (12 threads) - 15.84 GiB memory

### Issue description

At the moment, users can not rely on metadata to store information on their objects because this informartion is deleted when opening the project on a new machine.

### Steps to reproduce

1) download this project: https://github.com/Nodragem/top-down-action-adventure-starter-kit
2) move to the branch `metadata-bug`
3) open the project (there will be a lot of errors because of add-ons to be installed)
4) open `res://assets/objects/weapons/toy_gun/laser-gun-design1_Cube.tres`
5) observe that the metadata is empty

You can go and check that there should be metadata on the repository:
https://github.com/Nodragem/top-down-action-adventure-starter-kit/blob/main/assets/objects/weapons/toy_gun/laser-gun-design1_Cube.tres

Same issue is observed for:
https://github.com/Nodragem/top-down-action-adventure-starter-kit/blob/main/assets/objects/laboratory/building_pass.tres

### Minimal reproduction project (MRP)

https://github.com/Nodragem/top-down-action-adventure-starter-kit
(see instructions above)

Reproduce the issue using the linked top-down-action-adventure-starter-kit project on its metadata-bug branch. Inspect the metadata in assets/objects/weapons/toy_gun/laser-gun-design1_Cube.tres and assets/objects/laboratory/building_pass.tres before and after opening the project on a new machine. Done means the existing metadata remains available after opening the project.

Written by the indexing model from the issue text.