Fix Resource doesn't update when overwritten in editor

[beicause]

Partially addresses #30302, #104966 (comment)

After this PR, resources overwritten by EditorNode::save_resource_in_path can be updated in scenes, inspector and thumbnails correctly.

Note:

• Resources in the scene are still not be updated, but they can be updated by re-assigning the resources or reloading the scene. Resolved by EditorNode::replace_resources_in_scenes.
• Resources overwritten by tool scripts are still not updated, but this may be resolved by manually calling Resource.take_over_path and EditorFileSystem.update_file. However it has the above issue unless reloading resources in the scene.

[Repiteo]

Thanks!