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There are so many possibilities for this behaviour that you will blow your brains out trying to solve it all at conversion time.
It looks like you have already been in the Editor to see the code. Fix it there with search and replace. With each book you can see exactly what the offending lines are and blow them away. With a little practice it will only take a couple of minutes to fix a book.
After a few books you will almost certainly find repeating patterns...you can save searches for later use, and even edit a saved search on the fly for minor changes.
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