You need to be working in the theme's files only. Don't make those changes to, or delete any WordPress core files needlessly.
just can't find the words "comments are closed" exactly as it appears.
If you are seeing "Comments are closed." in black text on a white background, at the bottom of a post on a single page, below the post footer, and not in the footer bar, then I believe it is coming from here:
Line 164, comments.php, in the Atahualpa theme folder;
If you deleted it from the theme folder, I have no clue where it is comming from.
<?php
// END of "If comments are open, but there are no comments"
else :
// If comments are closed:
?>
<p><?php _e('Comments are closed.','atahualpa'); ?></p>
<?php endif; ?>
Remove Comments are closed. only and save the file. Leave the tick marks. It will look like this;
<p><?php _e('','atahualpa'); ?></p>
<?php endif; ?>
You can also find that line of code in the "comments-paged.php" for the obvious reasons.
If you are seeing "Comments are closed" in the post footer area (inside the grey border). You can make changes from here;
go the theme options page titled "Post/Page Info Items", and remove or modify the comments from the footer on both single and multi post pages as you see fit.
I'm out of ideas. Good luck.