Editable Children = on breaks paths to instanced SubViewports & manual fixes are not retained

### Tested versions

reproduced in 4.0.4.stable & 4.2.1.stable

### System information

Godot v4.2.1.stable unknown - Arch Linux #1 SMP PREEMPT_DYNAMIC Fri, 05 Jan 2024 16:20:41 +0000 - Tty - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1070 (nvidia; 545.29.06) - Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz (8 Threads)

### Issue description

If a scene instances another scene with "Editable Children" enabled, and the child scene contains a `SubViewport`, and a material rendering that `SubViewport`, the material's "Viewport Path" will be wrong. It'll render a magenta texture instead of the `SubViewport`. You can fix the path manually, but the editor revert to the wrong path after reloading.

### Steps to reproduce

The attached `subviewport_instance_tests.zip` has 2 Godot projects, `standard_project` & `shader_project`. They demonstrate the same problem, using a `StandardMaterial3D` and a `ShaderMaterial`. I tried both projects under Godot 4.0.4 & 4.2.1 and got the same results all 4 times.

Consider `standard_project`. Scene A has:
```
A
├ Camera3D
├ MeshInstance3D
└ SubViewport
├ Camera3D
└ Label3D (text = "A")
```
The `MeshInstance3D` displays the `SubViewport`. Running scene A (open a.tscn in the editor > right click the "a" tab > "Play This Scene") works as expected - "A" appears on the `MeshInstance3D`.

Scene B instances A:
```
B
├ Camera3D
└ A
```
Running scene B also works as expected.

Scene C is exactly like B, except C's A instance has "Editable Children" enabled. In C, the `MeshInstance3D` shows a solid magenta texture, and there's an error, "ViewportTexture: Path to node is invalid".

It seems that "Editable Children" causes the `ViewportTexture`'s `viewport_path` to be interpreted as an absolute path from the root (the C node).

I tested this with scene D. D is like C, except I added a `SubViewport` at that absolute path:
```
D
├ Camera3D
├ A
└ SubViewport
├ Camera3D
└ Label3D (text = "D")
```
Playing scene D, A's `MeshInstance3D` shows "D", not "A".

We can fix scenes C and D manually:
- Select the `MeshInstance3D`.
- In the inspector, go to "Geometry" > "Material Override" > "Albedo" > "Texture"
- change "Viewport Path" from "SubViewport" to "A/SubViewport".
- Run the scene.

Now C and D work as expected. But this only helps temporarily - certain combinations of opening, saving, & closing cause the `viewport_path` to revert. It's a bit hard to repro, but this sequence seems to trigger it pretty reliably:
- Do the manual fix on scene C.
- Save & close the whole project.
- Reopen the project.
- Close scene A.
- Reopen scene A.
- Save the whole project again.
- Return to scene C. The texture is magenta again, and "Viewport Path" has reverted to just "SubViewport".

You can try the same steps in `shader_project` and get the same result. The `ViewportTexture` is a `uniform` named `tex`. You can fix `tex` in the material inspector, but it also gets reverted.

### Minimal reproduction project (MRP)

[subviewport_instance_tests.zip](https://github.com/godotengine/godot/files/14120368/subviewport_instance_tests.zip)