$product->variations[] = array('target_id' => $referenced_variation->id());
    $product->save();

    $variation = Drupalcommerce_productEntityProductVariation::create([
       'type' => 'default',
       'sku' => 'to_be_deleted',
       'status' => 0,
       'price' => 0,
    ]);
    $variation->save();

    $product_to_delete->variations = array('target_id' => $variation->id());

    $product_to_delete->save();
    $product_to_delete->delete();