### 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)
int quad_size = tile_map_node->get_rendering_quadrant_size();
			const Vector2i &coords = r_cell_data.coords;
			
			quadrant_coords = Vector2i(
					coords.x > 0 ? coords.x / quad_size : (coords.x - (quad_size - 1)) / quad_size,
					coords.y > 0 ? coords.y / quad_size : (coords.y - (quad_size - 1)) / quad_size);
			canvas_items_position = quad_size * quadrant_coords;
		}
		Ref<RenderingQuadrant> rendering_quadrant;
		if (rendering_quadrant_map.has(quadrant_coords)) {
			
			rendering_quadrant = rendering_quadrant_map[quadrant_coords];
		} else {
			
			rendering_quadrant.instantiate();
			rendering_quadrant->quadrant_coords = quadrant_coords;
			rendering_quadrant->canvas_items_position = canvas_items_position;
			rendering_quadrant_map[quadrant_coords] = rendering_quadrant;
		}
		
		if (r_cell_data.rendering_quadrant.is_valid()) {
			if (!r_cell_data.rendering_quadrant->dirty_quadrant_list_element.in_list()) {
				r_dirty_rendering_quadrant_list.add(&r_cell_data.rendering_quadrant->dirty_quadrant_list_element);
			}
		}
		
		if (r_cell_data.rendering_quadrant_list_element.in_list()) {
			r_cell_data.rendering_quadrant_list_element.remove_from_list();
		}