Magento version 1 & 2, Locate Orphaned Records by Foreign Keys, and display SQL to Remove them.

removeOrphanFKs-m2.php

<?php

// USE WITH MAGENTO 2.X
// Edit function call with DB details
// Usage: php removeOrphanFKs.php
// Used in conjunction with Magento Data Migration Tool
//
// Original script from: David Grudl (https://github.com/dg/MySQL-check)
// Modified by: Jared Blalock (http://molotovbliss.com) 
//
// Adjust include for env.php and execute:
// php -f removeOrphanFks-m2.php


$config = include_once("../app/etc/env.php");
$dbConfig = $config['db']['connection']['default'];

$host = $dbConfig['host'];
$user = $dbConfig['username'];
$pass = $dbConfig['password'];
$db   = $dbConfig['dbname'];

// Locate Orphan Foreign Keys, echo the DELETE SQL Query and execute it
function checkForeignKeys(mysqli $db, $database = NULL)
{
	// get a list off all foreign keys from schema
	$keys = $db->query('SELECT TABLE_SCHEMA, TABLE_NAME, COLUMN_NAME, REFERENCED_TABLE_NAME, REFERENCED_COLUMN_NAME	FROM information_schema.KEY_COLUMN_USAGE WHERE REFERENCED_TABLE_SCHEMA IS NOT NULL'	. ($database ? " AND TABLE_SCHEMA='{$db->escape_string($database)}'" : ''));

	try {
		// loop over all fk
		foreach ($keys as $key) {
			foreach ($key as & $identifier) {
				$identifier = '`' . str_replace('`', '``', $identifier) . '`';
			}

			// detect orphans
			$sqlQuery = "SELECT COUNT($key[COLUMN_NAME]) FROM $key[TABLE_SCHEMA].$key[TABLE_NAME] WHERE $key[COLUMN_NAME] NOT IN (SELECT $key[REFERENCED_COLUMN_NAME] FROM $key[TABLE_SCHEMA].$key[REFERENCED_TABLE_NAME])";
			$row = @$db->query($sqlQuery)->fetch_array();
			if(is_array($row) && $row[0] >= 1) {
				echo $row[0] ? "-- $key[TABLE_SCHEMA] $key[TABLE_NAME].$key[COLUMN_NAME]: found $row[0] invalid foreign keys!".PHP_EOL : "";
				// orphans found remove them
				if($row[0]) {
					//$delQuery = "DELETE FROM $key[TABLE_SCHEMA].$key[TABLE_NAME] WHERE $key[COLUMN_NAME] NOT IN (SELECT $key[REFERENCED_COLUMN_NAME] FROM $key[TABLE_SCHEMA].$key[REFERENCED_TABLE_NAME])";
					$delQuery = "DELETE FROM $key[TABLE_NAME] WHERE $key[COLUMN_NAME] NOT IN (SELECT $key[REFERENCED_COLUMN_NAME] FROM $key[REFERENCED_TABLE_NAME])";
					echo $delQuery . PHP_EOL . PHP_EOL;
					//$db->query($delQuery); // uncomment out if you'd like to execute
				}
			}
		}
	} catch (Exception $e) {
		print_r($e);
	}	
}

checkForeignKeys(new mysqli($host, $user, $pass), $db);

removeOrphanFKs.php

<?php

// USE WITH MAGENTO 1.X
// Edit function call with DB details
// Usage: php removeOrphanFKs.php
// Used in conjunction with Magento Data Migration Tool
//
// Original script from: David Grudl (https://github.com/dg/MySQL-check)
// Modified by: Jared Blalock (http://molotovbliss.com) 
//
// Adjust DB details and execute:
// php -f removeOrphanFKs.php

$host = 'localhost';
$user = 'root';
$pass = 'password';
$db   = 'dbname';

// Locate Orphan Foreign Keys, echo the DELETE SQL Query and execute it
function checkForeignKeys(mysqli $db, $database = NULL)
{
	// get a list off all foreign keys from schema
	$keys = $db->query('SELECT TABLE_SCHEMA, TABLE_NAME, COLUMN_NAME, REFERENCED_TABLE_NAME, REFERENCED_COLUMN_NAME	FROM information_schema.KEY_COLUMN_USAGE WHERE REFERENCED_TABLE_SCHEMA IS NOT NULL'	. ($database ? " AND TABLE_SCHEMA='{$db->escape_string($database)}'" : ''));

	// loop over all fk
	foreach ($keys as $key) {
		foreach ($key as & $identifier) {
			$identifier = '`' . str_replace('`', '``', $identifier) . '`';
		}

		// detect orphans
		$sqlQuery = "SELECT COUNT($key[COLUMN_NAME]) FROM $key[TABLE_SCHEMA].$key[TABLE_NAME] WHERE $key[COLUMN_NAME] NOT IN (SELECT $key[REFERENCED_COLUMN_NAME] FROM $key[TABLE_SCHEMA].$key[REFERENCED_TABLE_NAME])";
		$row = $db->query($sqlQuery)->fetch_array();
		echo $row[0] ? "$key[TABLE_SCHEMA] $key[TABLE_NAME].$key[COLUMN_NAME]: found $row[0] invalid foreign keys!\n" : "";

		// orphans found remove them
		if($row[0]) {
			$delQuery = "DELETE FROM $key[TABLE_SCHEMA].$key[TABLE_NAME] WHERE $key[COLUMN_NAME] NOT IN (SELECT $key[REFERENCED_COLUMN_NAME] FROM $key[TABLE_SCHEMA].$key[REFERENCED_TABLE_NAME])";
			echo $delQuery;
			//$db->query($delQuery); // uncomment out if you'd like to execute
		}

	}
}

checkForeignKeys(new mysqli($host, $user, $pass), $db);