### 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)
DIRTY_FLAGS_TILE_MAP_QUADRANT_SIZE,
		DIRTY_FLAGS_TILE_MAP_COLLISION_ANIMATABLE,
		DIRTY_FLAGS_TILE_MAP_COLLISION_VISIBILITY_MODE,
		DIRTY_FLAGS_TILE_MAP_NAVIGATION_VISIBILITY_MODE,
		DIRTY_FLAGS_TILE_MAP_Y_SORT_ENABLED,
		DIRTY_FLAGS_TILE_MAP_RUNTIME_UPDATE,
		DIRTY_FLAGS_MAX,
	};
private:
	
	String name;
	bool enabled = true;
	Color modulate = Color(1, 1, 1, 1);
	bool y_sort_enabled = false;
	int y_sort_origin = 0;
	int z_index = 0;
	bool navigation_enabled = true;
	RID navigation_map;
	bool uses_world_navigation_map = false;
	
	TileMap *tile_map_node = nullptr;
	int layer_index_in_tile_map_node = -1;
	RID canvas_item;
	HashMap<Vector2i, CellData> tile_map;
	
	struct {
		bool flags[DIRTY_FLAGS_MAX] = { false };
		SelfList<CellData>::List cell_list;
	} dirty;
	bool in_destructor = false;