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For what it may be worth, an ePub MUST be encoded in UTF-8 or UTF-16 though I can count the number of UTF-16 encoded ePubs that I've seen over the last 15 years without needing to use more than both thumbs.
OTOH, I've seen ePubs encoded in whatever the local encoding used by the OS all too often. At least now, anyone who checks with epubcheck gets an error message (that covers most publishers and ebook creators/polishers).
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