### Godot version

v4.0.beta14.official [28a24639c]

### System information

Windows 10, OpenGL

### Issue description

Vulkan and Mobile:
![Godot_v4 0-beta14_win64_kEcRNiMfNJ](https://user-images.githubusercontent.com/7782218/213967627-8e8755d9-2fe2-43b3-b197-f9f2840b7580.gif)

OpenGL:
![Godot_v4 0-beta14_win64_MQ233TZuPq](https://user-images.githubusercontent.com/7782218/213967651-ae463a6f-c867-4312-bdf1-525e1d7def01.gif)

At first I thought it was related to `set_buffer()`, but it turned out that `set_instance_*` also work incorrectly.
Probably the custom information is also set incorrectly, but I haven't checked it yet.

### Steps to reproduce

* Open MRP
* In the editor, select `MeshInstance3D` node and change the `Count` property
* -- or --
* Start the project and move the slider

You can also switch the renderer to Vulkan and compare.

### Minimal reproduction project

[set_buffer().zip](https://github.com/godotengine/godot/files/10476834/set_buffer.zip)

mesh_owner.initialize_rid(p_rid, Mesh());
}
void MeshStorage::mesh_free(RID p_rid) {
	mesh_clear(p_rid);
	mesh_set_shadow_mesh(p_rid, RID());
	Mesh *mesh = mesh_owner.get_or_null(p_rid);
	ERR_FAIL_COND(!mesh);
	mesh->dependency.deleted_notify(p_rid);
	if (mesh->instances.size()) {
		ERR_PRINT("deleting mesh with active instances");
	}
	if (mesh->shadow_owners.size()) {
		for (Mesh *E : mesh->shadow_owners) {
			Mesh *shadow_owner = E;
			shadow_owner->shadow_mesh = RID();
			shadow_owner->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_MESH);
		}
	}
	mesh_owner.free(p_rid);
}
void MeshStorage::mesh_set_blend_shape_count(RID p_mesh, int p_blend_shape_count) {
	ERR_FAIL_COND(p_blend_shape_count < 0);
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	ERR_FAIL_COND(mesh->surface_count > 0); 
	mesh->blend_shape_count = p_blend_shape_count;
}
bool MeshStorage::mesh_needs_instance(RID p_mesh, bool p_has_skeleton) {