Hi,
You can try the following code by putting in functions.php file of currently active theme or using Code Snippets plugin on backend:
add_action('wpinv_invoice_print_after_line_items', 'wpinv_invoice_print_after_line_items_cb', 10, 1);
function wpinv_invoice_print_after_line_items_cb($invoice){
    if(!$invoice){
        return;
    }
	$notes = wpinv_get_invoice_notes( $invoice->ID );
	echo '<ul class="invoice_notes">';
	if ( $notes ) {
		foreach( $notes as $note ) {
			$is_customer_note = get_comment_meta( $note->comment_ID, '_wpi_customer_note', true );
			if($is_customer_note) {
				?>
                <li rel="<?php echo absint( $note->comment_ID ); ?>" class="">
                    <div class="note_content">
						<?php echo wpautop( wptexturize( wp_kses_post( $note->comment_content ) ) ); ?>
                    </div>
                </li>
				<?php
			}
		}
	}
	echo '</ul>';
}
Let me know if it helps or not.
Regards,
Patrik