### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
#ifndef TILE_SET_H
#define TILE_SET_H
#include "core/io/resource.h"
#include "core/object/object.h"
#include "core/templates/local_vector.h"
#include "core/templates/rb_set.h"
#include "scene/2d/light_occluder_2d.h"
#include "scene/main/canvas_item.h"
#include "scene/resources/concave_polygon_shape_2d.h"
#include "scene/resources/convex_polygon_shape_2d.h"
#include "scene/resources/image_texture.h"
#include "scene/resources/navigation_polygon.h"
#include "scene/resources/packed_scene.h"
#include "scene/resources/physics_material.h"
#include "scene/resources/shape_2d.h"
#ifndef DISABLE_DEPRECATED
#include "scene/resources/shader.h"
#endif
class TileMap;