### 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)
per_terrain_pattern_tiles[terrain_set][terrains_pattern].insert(cell);
							}
							
							for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
								CellNeighbor bit = CellNeighbor(i);
								if (is_valid_terrain_peering_bit(terrain_set, bit)) {
									int terrain = terrains_pattern.get_terrain_peering_bit(bit);
									if (terrain >= 0) {
										per_terrain_pattern_tiles[terrain_set][terrains_pattern].insert(cell);
									}
								}
							}
						}
					}
				}
			}
		}
		
		for (int i = 0; i < terrain_sets.size(); i++) {
			TileSet::TerrainsPattern empty_pattern(this, i);
			TileMapCell empty_cell;
			empty_cell.source_id = TileSet::INVALID_SOURCE;
			empty_cell.set_atlas_coords(TileSetSource::INVALID_ATLAS_COORDS);
			empty_cell.alternative_tile = TileSetSource::INVALID_TILE_ALTERNATIVE;
			per_terrain_pattern_tiles[i][empty_pattern].insert(empty_cell);
		}
		terrains_cache_dirty = false;
	}
}
void TileSet::_compute_next_source_id() {