Haloscan help forum had the answer - it hadn't actually deleted the old comments, it had just hidden them.
Here's how I did the code - the best way is to hide the Haloscan commenting service (which doesn't have the facility to delete spam comments) and reinstate the Blogger comments service, whilst retaining the Trackback facility.
<BlogItemCommentsEnabled>
<!-- hide Haloscan comment service
<a class="comment-link" href="http://www.haloscan.com/comments/nemeton/<$BlogItemNumber$>/" title="Comment" onclick="HaloScan('<$BlogItemNumber$>'); return false;">
<script type="text/javascript">postCount('<$BlogItemNumber$>'); </script></a> end hiding Haloscan comments-->
<-- this is the Trackback bit you want to keep -->
| <a class="comment-link" href="http://www.haloscan.com/tb/nemeton/<$BlogItemNumber$>/" title="Trackback" onclick="HaloScanTB('<$BlogItemNumber$>'); return false;"><script type="text/javascript">postCountTB('<$BlogItemNumber$>'); </script></a>
<!-- Trackback autodiscovery code
<rdf:Description
rdf:about="<$BlogItemPermalinkURL$>"
dc:identifier="<$BlogItemPermalinkURL$>"
dc:title="<$BlogItemTitle$>"
trackback:ping="http://haloscan.com/tb/nemeton/<$BlogItemNumber$>" />
</rdf:RDF>
-->
<!-- reinsert Blogger comment service -->
| <a href="<$BlogItemCommentCreate$>"
<$BlogItemCommentFormOnClick$>>
<$BlogItemCommentCount$> comments</a>
<!-- end of reinserting Blogger comments -->
</BlogItemCommentsEnabled>
<!-- hide Haloscan comment service
<a class="comment-link" href="http://www.haloscan.com/comments/nemeton/<$BlogItemNumber$>/" title="Comment" onclick="HaloScan('<$BlogItemNumber$>'); return false;">
<script type="text/javascript">postCount('<$BlogItemNumber$>'); </script></a> end hiding Haloscan comments-->
<-- this is the Trackback bit you want to keep -->
| <a class="comment-link" href="http://www.haloscan.com/tb/nemeton/<$BlogItemNumber$>/" title="Trackback" onclick="HaloScanTB('<$BlogItemNumber$>'); return false;"><script type="text/javascript">postCountTB('<$BlogItemNumber$>'); </script></a>
<!-- Trackback autodiscovery code
<rdf:Description
rdf:about="<$BlogItemPermalinkURL$>"
dc:identifier="<$BlogItemPermalinkURL$>"
dc:title="<$BlogItemTitle$>"
trackback:ping="http://haloscan.com/tb/nemeton/<$BlogItemNumber$>" />
</rdf:RDF>
-->
<!-- reinsert Blogger comment service -->
| <a href="<$BlogItemCommentCreate$>"
<$BlogItemCommentFormOnClick$>>
<$BlogItemCommentCount$> comments</a>
<!-- end of reinserting Blogger comments -->
</BlogItemCommentsEnabled>
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