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Prestidigitweeze - I suspect its the Smarten Punctuation feature see
calibre tips and tricks: ebook format conversion
Quote:
When this is selected before the conversion, all plain quotes, dashes and ellipsis are converted to their typographically correct equivalents. For example, plain quotes to curly quotes.
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Smarten Punctuation is also a feature of Polish Books, the Modify Plugin and the Book Editor
I don't think you can turn off ellipsis transform without losing the others - ie its all or nothing.
BR