Version 7 of WordPress SEO by Yoast removes the replytocom variables by default.
We’ve removed the option to turn off the replytocom variable. The replytocom feature in WordPress lets you reply to comments without activating JavaScript in your browser. However, every comment gets is own link and these could all end up in the search engines. So we now remove these variables by default.
To get the replytcom variables back we can add the following filter in our theme’s functions.php
add_filter( 'wpseo_remove_reply_to_com', '__return_false' );