So, i made a few changes to super_invoice.php and now all non empty comments (including admin comments) are included in the invoice. The code is as follows:

// Find any comments entered at checkout
// and display on invoice if they exist
$orders_history = $db->Execute("SELECT orders_status_id, date_added, customer_notified, comments
FROM " . TABLE_ORDERS_STATUS_HISTORY . "
WHERE orders_id = '" . $oID . "'
ORDER BY date_added");

while (!$orders_history ->EOF) {
// check if note is empty, if yes, then skip it
if ($orders_history->fields['comments'] != '') {
$display_notes[] = $orders_history->fields['comments'];
}
$orders_history->MoveNext();
}


In particular the while loop is included to find all non empty comments.

and then at the bottom these are displayed:

<?php if (count($display_notes)>0) {?>
<tr>
<td><?php echo zen_draw_separator('pixel_trans.gif', '1', '5'); ?></td>
</tr>
<tr>
<td class="main" colspan="2"><strong><?php echo HEADER_CUSTOMER_NOTES; ?></strong></td>
</tr>
<?php for($i=0; $i<count($display_notes);$i++) { ?>
<tr>
<td class="main" colspan="2"><?php echo $display_notes[$i]; ?></td>
</tr>
<?php } ?>
<?php } ?>
</table>