Jimm,
please check this story.
http://www.fictionalley.org/authors/bexis/HPATFE.html
I updated the plugin to the newest version, restarted calibre and then updated the story. The "Update epub if new chapters" option reduced my 6100+ pages story to 112 pages. Only the newest chapter has any text in it. All the preceding 87 chapters contain the chapter number and title and nothing else.