changing root type of inherited scene breaks reference without generating a warning

[betalars]

Tested versions

• reproducible in 4.2.1 stable

System information

nixos unstable

Issue description

When changing the root type of a inherited scene, it breaks the inheritance without generating a warning. This causes the inherited nodes to no longer be displayed yellow in the editor and it causes resources like 3D-models to be stored in the scene file, witch is undesirable when using git.

Godot now gives warnings to prevent certain actions that break inheritance, like renaming objects in the scene tree.

This issue could be resolved by adding that safeguard for this case too.

I would however much prefer being able to change the structure of inherited scenes a bit, as this is the only workaround I know to having to use .res files. (.res files right now are unusable with git due to #68672)

Steps to reproduce

1. Add a 3D Model to your Godot Project (I tested this with .gltf files)
2. Create a inherited scene from a 3D Model
3. change the type of the root node

Minimal reproduction project (MRP)

N/A