Something like that:

// 1. Display multiple upload file field
add_action( 'woocommerce_after_order_notes', 'add_custom_checkout_field' );
function add_custom_checkout_field($checkout) {
    echo '<div class="woocommerce-additional-fields__field-wrapper">';
       woocommerce_form_field('certificate', array(
        'type'      => 'file',
        'class'     => array('form-row-wide'),
        'label'     => __('Files', 'woocommerce'),
        'required'  => false,
        'multiple'  => 'multiple',
        'name'      => 'certificate[]', // as array
        'accept'    => '.pdf,.doc,.docx,.rtf,.txt',
    ), '');
    echo '</div>';
}

// 2. Save multiple uploaded files URL and name to order meta
add_action( 'woocommerce_checkout_create_order', 'save_checkout_uploaded_files', 10, 2 );
function save_checkout_uploaded_files( $order, $data ){
    if( !empty($_FILES['certificate']['name'][0]) ) {
        $uploaded_files = array();

        foreach ($_FILES['certificate']['name'] as $key => $value) {
            if ($_FILES['certificate']['error'][$key] === UPLOAD_ERR_OK) {
                $file = array(
                    'name'     => $_FILES['certificate']['name'][$key],
                    'type'     => $_FILES['certificate']['type'][$key],
                    'tmp_name' => $_FILES['certificate']['tmp_name'][$key],
                    'error'    => $_FILES['certificate']['error'][$key],
                    'size'     => $_FILES['certificate']['size'][$key]
                );

                // Handle upload safely using WP functions
                $upload = wp_handle_upload($file, array('test_form' => false));

                if (!isset($upload['error'])) {
                    $uploaded_files[] = array(
                        'file_url'  => $upload['url'],
                        'file_name' => $file['name']
                    );
                }
            }
        }
        if (!empty($uploaded_files)) {
            $order->update_meta_data( '_checkout_upload', $uploaded_files );
        }
    }
}

// 3. Helper function to display uploaded files as links
function display_uploaded_files_list($files) {
    if (!empty($files) && is_array($files)) {
        echo '<p>' . __("Files Uploaded:", 'woocommerce') . '</p><ul>';
        foreach ($files as $file) {
            printf('<li><a href="%s" target="_blank" rel="noopener noreferrer">%s</a></li>', esc_url($file['file_url']), esc_html($file['file_name']));
        }
        echo '</ul>';
    }
}

// 4. Display uploaded files in admin order page
add_action('woocommerce_admin_order_data_after_billing_address', 'display_uploaded_files_in_admin_orders');
function display_uploaded_files_in_admin_orders( $order ) {
    $uploaded_files = $order->get_meta( '_checkout_upload' );
    display_uploaded_files_list($uploaded_files);
}

// 5. Display uploaded files on thank you page
add_action('woocommerce_order_details_after_order_table', 'display_uploaded_files_in_thankyou');
function display_uploaded_files_in_thankyou( $order ) {
    $uploaded_files = $order->get_meta( '_checkout_upload' );
    display_uploaded_files_list($uploaded_files);
}

// 6. Display uploaded files in WooCommerce emails
add_action('woocommerce_email_customer_details', 'display_uploaded_files_in_email');
function display_uploaded_files_in_email( $order ) {
    $uploaded_files = $order->get_meta( '_checkout_upload' );
    display_uploaded_files_list($uploaded_files);
}