Suffix removal with setup script doesn't work

Question

Method inside InstallData.php/UpgradeData.php to remove suffix from product and catalog pages:

public function removeSuffix()
{
    $this->_config->saveConfig('catalog/seo/product_url_suffix', null, 'default', 0);
    $this->_config->saveConfig('catalog/seo/category_url_suffix', null, 'default', 0);
}

As you can see in screenshots below, in backend the changes have been made and the core_config_data table has the fields that it would have if it was done manually in backend, but in url_rewrite table paths don't get updated.

Product and category links still show up as e.g. http://test.dev/gear/bags.html with the suffix.

I have done sudo bin/magento indexer:reindex and also tried flushing cache.

---

The suffix fields in backend are changed after running script:

---

The core_config_data table has the fields that would normally be there if it was done manually:

---

The url_rewrite table paths are not being changed:

Answer 1

UPDATE:

This setup script will set the product and category suffix values to an empty string and will update the url_rewrite table accordingly (assuming the suffix values were not empty to begin with).

<?php

namespace Vendor\Module\Setup;

use Magento\Framework\App\State as AppState;
use Magento\Framework\Setup\ModuleContextInterface;
use Magento\Framework\Setup\ModuleDataSetupInterface;
use Magento\Framework\Setup\InstallDataInterface;

class InstallData implements InstallDataInterface
{
    protected $configFactory;

    protected $appState;

    public function __construct(
        \Magento\Config\Model\Config\Factory $configFactory,
        AppState $appState
    ){
        $this->configFactory = $configFactory;
        $this->appState = $appState;
    }

    public function install(ModuleDataSetupInterface $setup, ModuleContextInterface $context)
    {
        $setup->startSetup();

        $this->appState->setAreaCode('adminhtml');

        $config = $this->configFactory->create();
        $config->setDataByPath('catalog/seo/product_url_suffix', '');
        $config->save();

        $config = $this->configFactory->create();
        $config->setDataByPath('catalog/seo/category_url_suffix', '');
        $config->save();

        $setup->endSetup();
    }
}

Original answer:

There is an afterSave method that runs when saving those values in the admin. You could try saving the suffix values in the admin in the System Config section of the admin and see if that removes the suffix from the url_rewrite table.

Also note that in Magento 2 there is no longer a url_rewrite index process, so this may have something to do with the index not making any difference.