Can we see a sample page of what kind of information there is in the sidenotes? Would it really be that much of a problem if the sidenotes were presented before the paragraph, in a smaller font, with a frame, and with a generous left margin, for instance?
Sometimes the clients want what the clients want, sure, but part of your work is explaining to the clients why what they want might not be a good idea. If you were an architect and a client asked you for something unreasonable (insecure, too expensive, too hot in summer, against local law, hard to maintain...) you'd be expected to explain it to your client, and make sure it's what he really wants, no matter what.
In this case, an ePUB book is not something that will be read on a Nook or iPad and that's all. No, it's something that someone, somewhere, will want to read on a smartphone, someone else will need to read with a 24pt font, and another person will need a text-to-speech system to read it. The best solution for a printed book is often not the best solution for an ebook.
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