### 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)
ci = rs->canvas_item_create();
				rs->canvas_item_set_z_index(ci, RS::CANVAS_ITEM_Z_MAX - 1);
				rs->canvas_item_set_parent(ci, tile_map_node->get_canvas_item());
			}
			const Vector2 quadrant_pos = tile_map_node->map_to_local(debug_quadrant.quadrant_coords * TILE_MAP_DEBUG_QUADRANT_SIZE);
			Transform2D xform(0, quadrant_pos);
			rs->canvas_item_set_transform(ci, xform);
			for (SelfList<CellData> *cell_data_list_element = debug_quadrant.cells.first(); cell_data_list_element; cell_data_list_element = cell_data_list_element->next()) {
				CellData &cell_data = *cell_data_list_element->self();
				if (cell_data.cell.source_id != TileSet::INVALID_SOURCE) {
					_rendering_draw_cell_debug(ci, quadrant_pos, cell_data);
					_physics_draw_cell_debug(ci, quadrant_pos, cell_data);
					_navigation_draw_cell_debug(ci, quadrant_pos, cell_data);
					_scenes_draw_cell_debug(ci, quadrant_pos, cell_data);
				}
			}
		} else {
			
			if (ci.is_valid()) {
				rs->free(ci);
			}
			quadrant_list_element->remove_from_list();
			debug_quadrant_map.erase(debug_quadrant.quadrant_coords);
		}
		quadrant_list_element = next_quadrant_list_element;
	}
	dirty_debug_quadrant_list.clear();
	_debug_was_cleaned_up = false;
}
void TileMapLayer::_debug_quadrants_update_cell(CellData &r_cell_data, SelfList<DebugQuadrant>::List &r_dirty_debug_quadrant_list) {