That is the whole issue! If you start out creating your book, in Word or whatever, with the knowledge that it's going to become an eBook, you can keep it simple and auto-conversion may need very little intervention. If, however, you get 'clever' with the source, you're entering a minefield.
When I'm wearing my musician's hat, I see lots of discussion on how to 'fix in the mix'. I usually recommend going back and tracking the performance you wanted in the first place! There's a parallel in eBook construction.
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