This code removes duplicate custom options for all products. Use toggle for test and debug.

Magento-Product-CustomOptions-Duplicate-Remover.php

<?php
	$debug=0;
	$test=0;
  /*
    Code by Harshvardhan Malpani - https://harshmalpani.in
    Tested for Magento CE 1.9.x
    Date: 25/04/2017
    Use $debug and $test toggles to display messages. 
    This script will remove all duplicate custom options in each product (duplicate logic = same title for multiple custom options)
    */
  function array_dup($ar)
	{
		return array_unique(array_diff_assoc($ar,array_unique($ar)));
	}
	$mageFilename = 'app/Mage.php';
	require_once $mageFilename;
	ini_set('display_errors', 1);
	error_reporting(E_ALL & ~E_NOTICE);
	umask(0);
	Mage::app('admin');
	Mage::register('isSecureArea', 1);
	Mage::app()->setCurrentStore(Mage_Core_Model_App::ADMIN_STORE_ID);
	$c=0;$d=0;
	if($test==0)
	{
		$productsArr  = Mage::getModel('catalog/product')->getCollection()->setPageSize(20)->setCurPage(1); 
	}
	else
	{
		$productsArr  = Mage::getModel('catalog/product')->getCollection();
	}
	foreach ($productsArr as $productss)
	{
		$i=0;
		$product = Mage::getModel('catalog/product')->load($productss->getId());
		if($debug)
		{
			echo $productss->getId().'<br>';
		}
		$arr=array();
		foreach ($product->getOptions() as $k=>$value) 
		{
			
			$arr['name'][]= $value->getTitle();
			$arr['id'][]= $value->getId();
			$i++;
		}
		$result=array_intersect_assoc($arr[0],$arr[1]);
		if($test)
		{
			var_dump($arr);
			
			var_dump(array_dup($arr['name']));
		}
		$dupli=array_dup($arr['name']);
		foreach($dupli as $k=>$v)
		{ 
			foreach($product->getOptions() as $onelastride)
			{
                if($onelastride->getId()==$arr['id'][$k])
                {
					if($debug)
					{
						echo $onelastride->getTitle().' will be deleted.<br>';
					}
					$c++;
					$onelastride->delete();
					
				}
			}
			$product->save();
			
			$d++;
		}
	}
	echo $c .' options removed across '.$d.' products in store';
?>