### 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)

lod.edge_length = s.lods[i].edge_length;
		lod.index_data = Utilities::buffer_get_data(GL_ELEMENT_ARRAY_BUFFER, s.lods[i].index_buffer, s.lods[i].index_buffer_size);
		sd.lods.push_back(lod);
	}
	sd.bone_aabbs = s.bone_aabbs;
	if (mesh->blend_shape_count) {
		sd.blend_shape_data = Vector<uint8_t>();
		for (uint32_t i = 0; i < mesh->blend_shape_count; i++) {
			sd.blend_shape_data.append_array(Utilities::buffer_get_data(GL_ARRAY_BUFFER, s.blend_shapes[i].vertex_buffer, s.vertex_buffer_size));
		}
	}
	return sd;
}
int MeshStorage::mesh_get_surface_count(RID p_mesh) const {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND_V(!mesh, 0);
	return mesh->surface_count;
}
void MeshStorage::mesh_set_custom_aabb(RID p_mesh, const AABB &p_aabb) {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	mesh->custom_aabb = p_aabb;
	mesh->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_AABB);
}
AABB MeshStorage::mesh_get_custom_aabb(RID p_mesh) const {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND_V(!mesh, AABB());
	return mesh->custom_aabb;
}
AABB MeshStorage::mesh_get_aabb(RID p_mesh, RID p_skeleton) {