Until the next release you can search & replace these comments.
I used ReplaceEm to fix my archives with the following
Search/Replace table :
{}p</body>[^<]*<!-- Added by HTTrack --><meta [^>]*><!--
/Added by HTTrack -->[^<]*</html>
</body>{}e</html>
{}p<html>[^<]*<!-- Added by HTTrack --><meta [^>]*><!--
/Added by HTTrack -->[^<]*<head>
<html>{}e<head>
Copy these lines to a .txt file and import it from ReplaceEm
in a group. | 
