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Your process seems.... cumbersome.
You are using this path: Word --> PDF --> Calibre --> Sigil --> Treepress
You can better do the following: Word --> filtered HTML --> Sigil (with Flightcrew) --> Treepress (if you must...)
That will yield better results, since no conversion from PDF has to be made. That will always results in less than perfect conversions. If you use styles in Word, that will make your life a lot easier. You can remove a whole lot of crap from the filtered HTML, but it will result in a better file.
If you insist on use Calibre, you can better use the following path: Word --> RTF --> Calibre --> Sigil. That should yield to better results.
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