Magento 2 console command to find any configuration values missing a default/global value and sets them to null. This is a fix for issue #12097

RepairDefaultConfigCommand.php

<?php
/**
 * @author Kevin Mace (kevin.mace@sotechnology.co.uk). All rights reserved.
 */

namespace KevinMace\Framework\Console;

use Symfony\Component\Console\Command\Command;
use Magento\Framework\App\Filesystem\DirectoryList;
use Magento\Framework\Filesystem\DriverPool;
use Symfony\Component\Console\Input\InputArgument;

/**
 * Repair Default Config Command
 *
 * Finds any config values missing a default/global value and sets
 * them to null. This is a fix for issue #12097
 */
class RepairDefaultConfigCommand extends Command
{
    /**
     * @var \Symfony\Component\Console\Output\OutputInterface $output
     */
    protected $output;

    /**
    * @var \Symfony\Component\Console\Input\InputInterface $input
    */
    protected $input;

    /**
     * @var \Magento\Store\Model\Store
     */
    protected $store;

    /**
     * @var  \Magento\Store\Model\StoreManagerInterface $storeManager
     */
    protected $storeManager;

    /**
     * @var ConfigFactory
     */
    protected $ConfigFactory;

    /**
     * @var ConfigCollectionFactory
     */
    protected $ConfigCollectionFactory;

    /**
     * @param \Magento\Store\Model\StoreManagerInterface $storeManager
     */
    public function __construct(
        \Magento\Store\Model\StoreManagerInterface $storeManager,
        \Magento\Config\Model\Config\Factory $configFactory,
        \Magento\Config\Model\ResourceModel\Config\Data\CollectionFactory $configCollectionFactory
    ) {
        $this->storeManager = $storeManager;
        $this->configFactory = $configFactory;
        $this->configCollectionFactory = $configCollectionFactory;

        parent::__construct();
    }

    /**
     * Set the command name and description
     */
    protected function configure()
    {
        $this->setName('kevinmace:config:repair')
            ->setDescription(
                'Finds any config values missing a default value and sets them to null. This is a fix for issue #12097'
            );
    }

    /**
     * Fired when the command is run
     *
     * @param \Symfony\Component\Console\Input\InputInterface $input,
     * @param \Symfony\Component\Console\Output\OutputInterface $output
     *
     * @retun void
     */
    protected function execute(
        \Symfony\Component\Console\Input\InputInterface $input,
        \Symfony\Component\Console\Output\OutputInterface $output
    ) {
        $this->output = $output;
        $this->input = $input;
        $paths = [];
        $globalPaths = [];

        $configCollection = $this->configCollectionFactory
            ->create()
            ->addFieldToFilter('scope', ['neq' => 'default']);

        foreach ($configCollection as $config) {
            if (!in_array($config->getPath(), $paths)) {
                $paths[] = $config->getPath();
            }
        }

        $globalConfigCollection = $this->configCollectionFactory
            ->create()
            ->addFieldToFilter('scope', 'default')
            ->addFieldToFilter('path', ['in' => $paths]);

        foreach ($globalConfigCollection as $config) {
            if (!in_array($config->getPath(), $globalPaths)) {
                $globalPaths[] = $config->getPath();
            }
        }

        $missingPaths = array_diff($paths, $globalPaths);

        $this->output->writeln('<comment>' . count($missingPaths) . ' missing entries found</comment>');
        if (count($missingPaths)) {
            $this->output->writeln('<comment>Beginning process to add missing default entries</comment>');
        }

        foreach ($missingPaths as $path) {
            $config = $this->configFactory->create();
            $config->setDataByPath($path, null);
            $config->save();
            $this->output->writeln('<info>Default entry created for: "' . $path . '"</info>');
        }
    }
}