### 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)

MeshInstance *mi = mesh_instance_owner.get_or_null(p_rid);
	_mesh_instance_clear(mi);
	mi->mesh->instances.erase(mi->I);
	mi->I = nullptr;
	mesh_instance_owner.free(p_rid);
}
void MeshStorage::mesh_instance_set_skeleton(RID p_mesh_instance, RID p_skeleton) {
	MeshInstance *mi = mesh_instance_owner.get_or_null(p_mesh_instance);
	if (mi->skeleton == p_skeleton) {
		return;
	}
	mi->skeleton = p_skeleton;
	mi->skeleton_version = 0;
	mi->dirty = true;
}
void MeshStorage::mesh_instance_set_blend_shape_weight(RID p_mesh_instance, int p_shape, float p_weight) {
	MeshInstance *mi = mesh_instance_owner.get_or_null(p_mesh_instance);
	ERR_FAIL_COND(!mi);
	ERR_FAIL_INDEX(p_shape, (int)mi->blend_weights.size());
	mi->blend_weights[p_shape] = p_weight;
	mi->dirty = true;
}
void MeshStorage::_mesh_instance_clear(MeshInstance *mi) {