Repository: godot
Issue: Changing properties of any 3d model and closing scene without saving persist (at least partially).
Labels: bug,discussion,topic:editor,usability

### Godot version

(mono) 4.0 b1, b2

### System information

Windows 10, Nvidia GTX 1660Ti, Vulkan

### Issue description

The title is a bit strange, I think the video will show the issues best so please check it out first.
Video: https://youtu.be/QHuqMWRdbDg

If you create a model or import one as a separate scene, instance it in a parent scene, then change any of its properties and then close the scene but click `don't save` if you check your model in the parent scene you will see the changes were kept as if the file was saved but if you open the closed scene of the model again it will update properly.

In the video please node how even the small preview window of the Mesh takes a while to update even after opening the scene again.

Also note that some changes remained saved while some return to original state.

Also note that first half of the video the changes actually seem to be getting saved although I click on don't save but when I return back to the scenes by opening them through FileSystem they are back to their initial states without changes.

As you can see it's quite a mess to describe this since sometimes it does what I describbed above sometimes it works even less.

Also Note how the small preview image of a closed scene bugs me as it gets stuck on the screen until I move my mouse cursor over a scene tab names (well I assume this might be a different bug but for now I'll keep it here until someone says it's not related).

As you can see in the video I never save any scene but changes still stay until I start doing something again.

What is not seen in the video but also can happen is that the small preview of the mesh when you click on the MeshInstance3D in the Inspector section `Mesh` sometimes doesn't change back to it's original color even after everything else changes (it seems it doesn't always update) but I did not manage to catch on the video unfortunately.

### Steps to reproduce

1. Add a model (MeshInstance3d) into your main scene, save the mesh instance as a separate scene.
2. Open the MeshInstance3d scene
3. Change Albedo color to something else
4. Close the scene but DON'T save the scene
5. Go back to the main scene from step 1 where you have your instance of the mesh instance and observe it's color has changed although you did not save the change
6. Repeat with some other properties as you can see in the video you can remove the top cap of a cylinder for example without changing)
7. Open the MeshInstance scene through the button next to the node name in the Scene docker observer it either returns back to original state or the changes remain (as in the video, it's kinda random, no idea what trigger what).
8. Close all the scene tabs and open them anew, you will see your modesl back in their original state everywhere

### Minimal reproduction project

No special project is needed for this, I've done all this in beta 1 as well as beta 2 mono (C#) but here is my scene with an external model just in case someone wants to test, the model is mine so feel free to use it as you see fit no need to hold back.

[TestNoSave.zip](https://github.com/godotengine/godot/files/9748266/TestNoSave.zip)