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One thing to try is to convert the ePub > ePub in Calibre and see how the code ends up. You might be able to easily edit the code from there.
Another thing to try is to remove unused CSS and use the new feature "Merge CSS rules with identical properties" in case there are a lot of CSS styles the same with different names. But you need to be using the current Calibre 5 for this to work.
And finally, if the format of the eBook is not complex, just drop the styles and make your own.
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