The rules for ISBNs say that every different edition should have its own ISBN - so hardcovers had a different ISBN to paperbacks and so on. With ebooks I have seen people say that a Kindle version should technically have a different ISBN to a epub, but I've also see others that say not. Since Amazon don't care much about the ISBN anyway, I have used the same ISBN. (All my ebooks, currently, come from the one source epub, so I think this approach is justified.)
If, however, I were to submit a Word document to Smashwords and let them meatgrind it into their dozen other formats - and if I wanted those to have an ISBN - then I believe they should have a separate ISBN to my original epub, because such versions are, realistically, a new edition.
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