This has been asked many times before but with no working answer.
I have multiple stores and some attributes have been overridden. I want to change these attributes
This doesn't work because you need the current store being the admin store for this kind of operation.
To make a specific store view use the default value for a given attribute:
Mage::app()->setCurrentStore(Mage_Core_Model_App::ADMIN_STORE_ID);
$product = Mage::getModel('catalog/product')
->load($product_id) // in your case: 1
->setStoreId($store_id) // in your case: 3
->setData($attr, false) // in your case: 'name'
->save();