### 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)

for (uint32_t i = 0; i < mi->surfaces.size(); i++) {
		if (mi->surfaces[i].version_count != 0) {
			for (uint32_t j = 0; j < mi->surfaces[i].version_count; j++) {
				glDeleteVertexArrays(1, &mi->surfaces[i].versions[j].vertex_array);
				mi->surfaces[i].versions[j].vertex_array = 0;
			}
			memfree(mi->surfaces[i].versions);
		}
		if (mi->surfaces[i].vertex_buffers[0] != 0) {
			GLES3::Utilities::get_singleton()->buffer_free_data(mi->surfaces[i].vertex_buffers[0]);
			GLES3::Utilities::get_singleton()->buffer_free_data(mi->surfaces[i].vertex_buffers[1]);
			mi->surfaces[i].vertex_buffers[0] = 0;
			mi->surfaces[i].vertex_buffers[1] = 0;
		}
		if (mi->surfaces[i].vertex_buffer != 0) {
			GLES3::Utilities::get_singleton()->buffer_free_data(mi->surfaces[i].vertex_buffer);
			mi->surfaces[i].vertex_buffer = 0;
		}
	}
	mi->surfaces.clear();
	mi->blend_weights.clear();
	mi->skeleton_version = 0;
}
void MeshStorage::_mesh_instance_add_surface(MeshInstance *mi, Mesh *mesh, uint32_t p_surface) {