I'm not a Calibre super user and for this kind of a task I would rather use Sigil. Sigil is built specifically for generating ePub...
Edit: You may need to rebuild the index.html file (i.e., use find/replace to update the links to the files).
Edit2: Just add all the HTML files to Sigil and then order them if necessary (by dragging and dropping them on the left pane). Sigil creates a directory structure so that all HTML files are under a Text/ folder. So, you need to update the links to use that path instead: If the original links were like "C:\mydir\file1.html", the new location will be "..\Text\file1.html" and you can run a Find/Replace over all files that replaces "C:\mydir\" with "..\Text\".
If you also have images, those also need to be added (and they are located in a folder called Image\. You can repeat the Find/Replace for those files.
Last edited by canpolat; 09-09-2014 at 08:40 AM.
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