### 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_V(!mesh, RS::BLEND_SHAPE_MODE_NORMALIZED);
	return mesh->blend_shape_mode;
}
void MeshStorage::mesh_surface_update_vertex_region(RID p_mesh, int p_surface, int p_offset, const Vector<uint8_t> &p_data) {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	ERR_FAIL_UNSIGNED_INDEX((uint32_t)p_surface, mesh->surface_count);
	ERR_FAIL_COND(p_data.size() == 0);
	uint64_t data_size = p_data.size();
	ERR_FAIL_COND(p_offset + data_size > mesh->surfaces[p_surface]->vertex_buffer_size);
	const uint8_t *r = p_data.ptr();
	glBindBuffer(GL_ARRAY_BUFFER, mesh->surfaces[p_surface]->vertex_buffer);
	glBufferSubData(GL_ARRAY_BUFFER, p_offset, data_size, r);
	glBindBuffer(GL_ARRAY_BUFFER, 0);
}
void MeshStorage::mesh_surface_update_attribute_region(RID p_mesh, int p_surface, int p_offset, const Vector<uint8_t> &p_data) {
	Mesh *mesh = mesh_owner.get_or_null(p_mesh);
	ERR_FAIL_COND(!mesh);
	ERR_FAIL_UNSIGNED_INDEX((uint32_t)p_surface, mesh->surface_count);
	ERR_FAIL_COND(p_data.size() == 0);
	uint64_t data_size = p_data.size();
	ERR_FAIL_COND(p_offset + data_size > mesh->surfaces[p_surface]->attribute_buffer_size);
	const uint8_t *r = p_data.ptr();
	glBindBuffer(GL_ARRAY_BUFFER, mesh->surfaces[p_surface]->attribute_buffer);
	glBufferSubData(GL_ARRAY_BUFFER, p_offset, data_size, r);
	glBindBuffer(GL_ARRAY_BUFFER, 0);
}
void MeshStorage::mesh_surface_update_skin_region(RID p_mesh, int p_surface, int p_offset, const Vector<uint8_t> &p_data) {