### 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)

return skeleton_owner.allocate_rid();
}
void MeshStorage::skeleton_initialize(RID p_rid) {
	skeleton_owner.initialize_rid(p_rid, Skeleton());
}
void MeshStorage::skeleton_free(RID p_rid) {
	_update_dirty_skeletons();
	skeleton_allocate_data(p_rid, 0);
	Skeleton *skeleton = skeleton_owner.get_or_null(p_rid);
	skeleton->dependency.deleted_notify(p_rid);
	skeleton_owner.free(p_rid);
}
void MeshStorage::_skeleton_make_dirty(Skeleton *skeleton) {
	if (!skeleton->dirty) {
		skeleton->dirty = true;
		skeleton->dirty_list = skeleton_dirty_list;
		skeleton_dirty_list = skeleton;
	}
}
void MeshStorage::skeleton_allocate_data(RID p_skeleton, int p_bones, bool p_2d_skeleton) {
	Skeleton *skeleton = skeleton_owner.get_or_null(p_skeleton);
	ERR_FAIL_COND(!skeleton);
	ERR_FAIL_COND(p_bones < 0);
	if (skeleton->size == p_bones && skeleton->use_2d == p_2d_skeleton) {
		return;
	}
	skeleton->size = p_bones;
	skeleton->use_2d = p_2d_skeleton;
	skeleton->height = (p_bones * (p_2d_skeleton ? 2 : 3)) / 256;
	if ((p_bones * (p_2d_skeleton ? 2 : 3)) % 256) {