Use this snippet to allow bundled item discounts over sale prices.

woocommerce-bundles-discount-over-sale-prices.php

<?php
/**
 * Plugin Name: WooCommerce Product Bundles - Discounts over Sale Prices
 * Plugin URI: https://woocommerce.com/products/product-bundles/
 * Description: Use this snippet to allow bundled item discounts over sale prices.
 * Version: 1.0
 * Author: SomewhereWarm
 * Author URI: https://somewherewarm.gr/
 * Developer: Manos Psychogyiopoulos
 *
 * Requires at least: 3.8
 * Tested up to: 4.8
 *
 * Copyright: © 2017-2020 SomewhereWarm SMPC ([email protected]).
 * License: GNU General Public License v3.0
 * License URI: http://www.gnu.org/licenses/gpl-3.0.html
 */
 
// To use this snippet, download this file into your plugins directory and activate it, or copy the code under this line into the functions.php file of your (child) theme.
 
add_filter( 'woocommerce_bundled_item_discount_from_regular', 'wc_pb_bundled_item_discount_from_regular', 10, 2 );

function wc_pb_bundled_item_discount_from_regular( $from_regular, $bundled_item ) {
	return false;
}