### 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)

Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	Mesh *shadow_mesh = mesh_owner.get_or_null(mesh->shadow_mesh);
	if (shadow_mesh) {
		shadow_mesh->shadow_owners.erase(mesh);
	}
	mesh->shadow_mesh = p_shadow_mesh;
	shadow_mesh = mesh_owner.get_or_null(mesh->shadow_mesh);
	if (shadow_mesh) {
		shadow_mesh->shadow_owners.insert(mesh);
	}
	mesh->dependency.changed_notify(Dependency::DEPENDENCY_CHANGED_MESH);
}
void MeshStorage::mesh_clear(RID p_mesh) {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	
	for (MeshInstance *mi : mesh->instances) {
		_mesh_instance_clear(mi);
	}
	for (uint32_t i = 0; i < mesh->surface_count; i++) {
		Mesh::Surface &s = *mesh->surfaces[i];
		if (s.vertex_buffer != 0) {
			GLES3::Utilities::get_singleton()->buffer_free_data(s.vertex_buffer);
			s.vertex_buffer = 0;
		}
		if (s.version_count != 0) {
			for (uint32_t j = 0; j < s.version_count; j++) {
				glDeleteVertexArrays(1, &s.versions[j].vertex_array);
				s.versions[j].vertex_array = 0;