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What OS are you using and what other tools do you have?
Select the book in Calibre and right click and choose "Tweak Epub" or just use the "T" key.
Copy the HTML files to another folder and use a word processor that can handle HTML files (like Word) to combine the files and convert them to RTF. Then re-import to Calibre and merge files.
Basically, if you can't get Calibre to convert it properly try other software until you find what works.
Calibre is a great swiss army knife but some files just don't convert well.
Happy Wednesday
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