Magento – How to remove default store view code from URL in Magento 2.1

Here is a more programattic method. It still skirts Magento's save() methods and the beforeSave/afterSave events but this works great and I use it sometimes in development to reset product data.

<?php 

    /** store id from which you would like to remove values */
    $storeId = 1;

    /** example attribute codes that you would to remove values for */
    $attributeCodesToReset = array('name', 'description');

    $model        = Mage::getModel('catalog/product');
    $resource     = $model->getResource();
    $entityTypeId = $resource->getEntityType()->getEntityTypeId();
    $adapter      = $resource->getWriteConnection();

    /** use collection(filter it appropriately) to grab product ids */
    $collection = $model->getCollection();
    $collection->addFieldToFilter('entity_id', 886);
    $collection->setStoreId($storeId);
    $productIds = $collection->getAllIds();

    foreach($attributeCodesToReset as $attributeCode) {
        $attribute = $resource->getAttribute($attributeCode);
        $condition = array(
            'entity_id IN(?)'    => $productIds,
            'attribute_id = ?'   => $attribute->getId(),
            'store_id = ?'       => $storeId,
            'entity_type_id = ?' => $entityTypeId
        );
        $adapter->delete($attribute->getBackendTable(), $condition);
    }

Update

This is how you would delete all attribute values from ALL NON-DEFAULT stores for products whose SKU begins with '16-'

/** store id for which you would like to KEEP values */
$defaultStoreId = Mage_Catalog_Model_Product::DEFAULT_STORE_ID;

/** @var Mage_Catalog_Model_Product $model */
$model        = Mage::getModel('catalog/product');
$resource     = $model->getResource();
$entityType   = $resource->getEntityType();
$entityTypeId = $entityType->getEntityTypeId();
$adapter      = $resource->getWriteConnection();

/** gather the names of all tables that contain the attribute values to be removed */
$tables = array();

/** get all attribute value tables, making sure to leave out catalog_product_entity */
$attributes = $entityType->getAttributeCollection();
$attributes->addFieldToFilter('backend_type', array('neq' => 'static'));
foreach($attributes as $attribute) {
    /** @var Mage_Catalog_Model_Resource_Eav_Attribute $attribute */
    $tables[] = $attribute->getBackendTable();
}
$tables = array_unique($tables);

/** get product ids of all products whose SKU begins with 16- */
$collection = $model->getCollection();
$collection->addFieldToFilter('sku', array('like' => '16-%'));
$productIds = $collection->getAllIds();

$valuesDeletedCount = 0;
foreach($tables as $table) {
    $condition = array(
        'entity_type_id = ?' => $entityTypeId, // here we ensure that we are only dealing with values belonging to PRODUCTS
        'entity_id IN(?)'    => $productIds, // here we make sure that we are only dealing with SKUs beginning with 16-
        'store_id != ?'      => $defaultStoreId, // here we make sure we are deleting from ALL stores except for DEFAULT
    );
    $valuesDeletedCount += $adapter->delete($table, $condition);
}
echo $valuesDeletedCount . ' non-default attribute values deleted.';

Turn off store code urls in admin

admin > stores > configuration > General > Web > Add Store Code to Urls > No

run upgrade, static-content-deply and cache clean/flush commands