This function will add zip files back to the allowed mime types WooCommerce can use

give_zip_back_to_wc.php

<?php // Only copy this line if needed

/**
 * This function will add zip files back to the allowed mime types WooCommerce can use
 * 
 * @param  array $mimes The allowed mime types
 * @return array        The filtered allowed mime types
 */
function give_zip_back_to_wc( $mimes ) {

	if ( ! isset( $mimes['zip'] ) || 'application/zip' != $mimes['zip'] ) {
		$mimes['zip'] = 'application/zip';
	}

	return $mimes;
}
add_filter( 'woocommerce_downloadable_file_allowed_mime_types', 'give_zip_back_to_wc', 999 );