### 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)
#endif 
	_clear_runtime_update_tile_data();
	
	for (int i = 0; i < DIRTY_FLAGS_MAX; i++) {
		dirty.flags[i] = false;
	}
	
	Vector<Vector2i> to_delete;
	for (SelfList<CellData> *cell_data_list_element = dirty.cell_list.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) {
			to_delete.push_back(cell_data.coords);
		}
	}
	
	for (const Vector2i &coords : to_delete) {
		tile_map.erase(coords);
	}
	
	dirty.cell_list.clear();
}
void TileMapLayer::set_cell(const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {
	
	Vector2i pk(p_coords);
	HashMap<Vector2i, CellData>::Iterator E = tile_map.find(pk);
	int source_id = p_source_id;
	Vector2i atlas_coords = p_atlas_coords;
	int alternative_tile = p_alternative_tile;
	if ((source_id == TileSet::INVALID_SOURCE || atlas_coords == TileSetSource::INVALID_ATLAS_COORDS || alternative_tile == TileSetSource::INVALID_TILE_ALTERNATIVE) &&