I just want to quote this well written post in the ePub section about using Calibre to do ePub > ePub conversions.
Quote:
Originally Posted by Toxaris
In some cases conversion within Calibre will break things that are perfectly fine to begin with. So, it adds unnecessary code and potentially breaks things. If your ePUB is not working, you should solve it in the source instead on relying on a Calibre conversion.
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