Jim,
I'm not a fanfiction reader, but my wife is, so I had a play with your plugin. I tested it with a couple of the links posted here to see how it went and I am very impressed (and amused by the short Dr Who story).
One thing that occurred to me, do you keep the bookmarks that the Calibre viewer puts into the epub? One of the bookmarks is the current reading location, I can see that if the story is being updated with new chapters, if the bookmarks are lost it could get very annoying. If you haven't seen them, the bookmarks are in the file "calibre_bookmarks.txt" in the "META-INF" folder of the epub.
And I just had a look at the story again. On the title page, you have "Categoryq". Is that a typo?
David
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