I had the same problem on the Kobo with epub - I have found that it's easier to leave the books in PDF format. If I knew what fonts the Kobo used I could call up the hex code or whatever for the Greek letter, but without that information, difficult and I am not sure that the fonts it uses even have Greek diacritics. I guess as our needs are rather ""minority" we are probably not going to see a special software fix!
The other strange workaround might be to cut and past the Greek text as an image, messy but worth a try if it is vital to the book.
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