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I understand not wanting to smarten a whole book as a test. Backups or not. You couldn't possibly know what might have gone wrong without then proofreading the entire book for potential problems. No fun.
I recommend making a test ePub that consists of only one page. On that page, throw every possible scenario you can think of (a paragraph or even a sentence at a time), "smarten" it and check the results.
Repeat until you are satisfied you know what's going on.
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