### 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)

s.blend_shapes[j].vertex_buffer = 0;
				}
				if (s.blend_shapes[j].vertex_array != 0) {
					glDeleteVertexArrays(1, &s.blend_shapes[j].vertex_array);
					s.blend_shapes[j].vertex_array = 0;
				}
			}
			memdelete_arr(s.blend_shapes);
		}
		if (s.skeleton_vertex_array != 0) {
			glDeleteVertexArrays(1, &s.skeleton_vertex_array);
			s.skeleton_vertex_array = 0;
		}
		memdelete(mesh->surfaces[i]);
	}
	if (mesh->surfaces) {
		memfree(mesh->surfaces);
	}
	mesh->surfaces = nullptr;
	mesh->surface_count = 0;
	mesh->material_cache.clear();
	mesh->has_bone_weights = false;
	mesh->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_MESH);
	for (Mesh *E : mesh->shadow_owners) {
		Mesh *shadow_owner = E;
		shadow_owner->shadow_mesh = RID();
		shadow_owner->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_MESH);
	}
}
void MeshStorage::_mesh_surface_generate_version_for_input_mask(Mesh::Surface::Version &v, Mesh::Surface *s, uint32_t p_input_mask, MeshInstance::Surface *mis) {