### 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)
if (p_a.y == p_b.y) {
				return p_a.x > p_b.x;
			} else {
				return p_a.y < p_b.y;
			}
		}
	};
	Vector2i quadrant_coords;
	SelfList<CellData>::List cells;
	List<RID> canvas_items;
	Vector2 canvas_items_position;
	SelfList<RenderingQuadrant> dirty_quadrant_list_element;
	
	RenderingQuadrant(const RenderingQuadrant &p_other) :
			dirty_quadrant_list_element(this) {
		quadrant_coords = p_other.quadrant_coords;
		cells = p_other.cells;
		canvas_items = p_other.canvas_items;
	}
	RenderingQuadrant() :
			dirty_quadrant_list_element(this) {
	}
	~RenderingQuadrant() {
		cells.clear();
	}
};
class TileMapLayer : public RefCounted {