I have been experimenting with multiple HTML files and ran into problems. It took me a while to figure it out -and it may still be a fault on my part!
Using SoftSnow as recommended above, I merged my 70 odd html files but could not get the ePub to work correctly with Calibre.
Then I noticed that SoftSnow had left the </body></html> at the end of every segment, whereas the merged file should have only one instance, at the end of the file. Removing the extras has cured my ePub problem.
I hope that this helps others.
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