Add a "download all" option to emails for WooCommerce downloadable products. Zips all the files and stores the zip in a specified directory.

create-zip.php

<?php
/**
 * Utility function to create a zip file from an array of file URLs
 * Used for download links in emails
 * @param array $files
 * @param string $filename
 *
 * @return string
 */
function doublee_zip_order_files(array $files, string $filename) {
	$upload_dir = $YOUR_DIRECTORY_HERE; // IMPORTANT: Ensure protection on this directory to ensure only authorised users can download the zip file.
	$zip_path = $upload_dir['path'] . '/' . $filename;
	$zip_url = $upload_dir['url'] . '/' . $filename;
	$zip = new ZipArchive;

	// Create the zip file
	$zip->open($zip_path, ZipArchive::CREATE | ZipArchive::OVERWRITE);

	// Loop through the files, get the WP attachment and path, and use these to add the files to the zip
	foreach($files as $url) {
		$url_pieces = parse_url($url);
		$url_path = $url_pieces['path'];
		$path_pieces = explode('/', $url_path);
		$year_month_file = array_splice($path_pieces, -3);
		$year = $year_month_file[0];
		$month = $year_month_file[1];
		$file = $year_month_file[2];

		$args = array(
			'post_type'		=> 'attachment',
			'post_status'	=> 'inherit',
			'meta_query'	=> array(
				array(
					'key' 		=> '_wp_attached_file',
					'value' 	=> $year . '/' . $month . '/' . $file,
					'compare' 	=> 'LIKE',
				)
			),
			'fields'	=> 'ids'
		);
		$query = new WP_Query($args);
		$attachment_id = $query->posts[0];
		$path = get_attached_file($attachment_id);

		$zip->addFile($path, basename($path));
	}

	// Close the zip, we're done here
	$zip->close();

	// Return the zip URL
	return $zip_url;
}

email-downloads.php

<?php
/**
 * Email Downloads.
 *
 * This template can be overridden by copying it to yourtheme/woocommerce/emails/email-downloads.php.
 *
 * HOWEVER, on occasion WooCommerce will need to update template files and you
 * (the theme developer) will need to copy the new files to your theme to
 * maintain compatibility. We try to do this as little as possible, but it does
 * happen. When this occurs the version of the template file will be bumped and
 * the readme will list any important changes.
 *
 * @see https://docs.woocommerce.com/document/template-structure/
 * @package WooCommerce/Templates
 * @version 3.4.0
 */

defined( 'ABSPATH' ) || exit;

$text_align = is_rtl() ? 'right' : 'left';

// Create an array of unique downloads for the single-file list
$unique_downloads = array_unique_multidimensional($downloads, 'product_id');

// Prepare filename for our "Download All" zip file
// My client requested site name and order number, but for other use cases something random would provide more security through obscurity
$order_number = $order->get_order_number();
$filename = str_replace(' ', '-', get_bloginfo('name')) . '-' . $order_number . '.zip';

// Put all the file URLs into an array
$files = array();
foreach($downloads as $download) {
	array_push($files, $download['file']['file']);
}

// Only include each file once
$files = array_unique($files);

// Zip them and return the URL using our utility function
$zip_url = doublee_zip_order_files($files, $filename);
?>

<h2 class="woocommerce-order-downloads__title"><?php esc_html_e( 'Downloads', 'woocommerce' ); ?></h2>

<table class="td" cellspacing="0" cellpadding="6" style="width: 100%; font-family: 'Helvetica Neue', Helvetica, Roboto, Arial, sans-serif; margin-bottom: 40px;" border="1">
	<thead>
		<tr>
			<?php foreach ( $columns as $column_id => $column_name ) : ?>

				<?php 
				// Add the "Download all" link
				if($column_name=='Download'): ?>
					<th class="td" scope="col" style="text-align:<?php echo esc_attr( $text_align ); ?>;">
					<a href="<?= $zip_url ?>">Download All</a>
					</th>
				<?php else: ?>
					<th class="td" scope="col" style="text-align:<?php echo esc_attr( $text_align ); ?>;"><?php echo esc_html( $column_name ); ?></th>
				<?php endif; ?>
				
			<?php endforeach; ?>
		</tr>
	</thead>

	<?php 
	// List the individual downloads
	foreach ($unique_downloads as $download) : ?>
		<tr>
			<?php foreach ( $columns as $column_id => $column_name ) : ?>
				<td class="td" style="text-align:<?php echo esc_attr( $text_align ); ?>;">
					<?php
					if ( has_action( 'woocommerce_email_downloads_column_' . $column_id ) ) {
						do_action( 'woocommerce_email_downloads_column_' . $column_id, $download, $plain_text );
					} else {
						switch ( $column_id ) {
							case 'download-product':
								?>
								<?php echo wp_kses_post( $download['product_name'] ); ?>
								<?php
								break;
							case 'download-file':
								?>
								<a href="<?php echo esc_url( $download['download_url'] ); ?>" class="woocommerce-MyAccount-downloads-file button alt"><?php echo esc_html( $download['download_name'] ); ?></a>
								<?php
								break;
							case 'download-expires':
								if ( ! empty( $download['access_expires'] ) ) {
									?>
									<time datetime="<?php echo esc_attr( date( 'Y-m-d', strtotime( $download['access_expires'] ) ) ); ?>" title="<?php echo esc_attr( strtotime( $download['access_expires'] ) ); ?>"><?php echo esc_html( date_i18n( get_option( 'date_format' ), strtotime( $download['access_expires'] ) ) ); ?></time>
									<?php
								} else {
									esc_html_e( 'Never', 'woocommerce' );
								}
								break;
						}
					}
					?>
				</td>
			<?php endforeach; ?>
		</tr>
	<?php endforeach; ?>
</table>

utilities.php

<?php
/**
 * array_unique for a multi-dimensional array
 * @see https://stackoverflow.com/a/34283567/6913674
 * @param $array
 * @param $key
 *
 * @return array
 */
function array_unique_multidimensional($array, $key) {
	$i = 0;
	$new_array = array();
	$key_array = array();

	foreach($array as $val) {
		if(!in_array($val[$key],$key_array)){
			$key_array[$i] = $val[$key];
			$new_array[$i] = $val;
		}
		$i++;
	}

	return $new_array;
}