There is of course the possibility to reset the template, but then you loose all customizations. So here's how I could enable Blogger threaded commenting on blogs where it did not work, due to previous customizations.
First you should check, that you have embedded comment form enabled, and also full blog feeds. Without those settings the threaded commenting won't show. If they are ok, and still no threaded comments, you should edit the template.
Open template html for editing, and click "Expand Widget Templates". Find this code, it is either twice or four times in the template:
<b:include data='post' name='comments'/>
Change every instance you find to this:
<b:if cond='data:post.showThreadedComments'>
<b:include data='post' name='threaded_comments'/>
<b:else/>
<b:include data='post' name='comments'/>
</b:if>
Save the template and test. If the previous changes were not enough, then you should see if this block of code is found, where threading javascript is included, and insert/modify it if necessary (search for <div id='comment-holder'>):
<div class='comments-content'>
<b:if cond='data:post.embedCommentForm'>
<b:include data='post' name='threaded_comment_js'/>
</b:if>
<div id='comment-holder'>
<data:post.commentHtml/>
</div>
</div>