Could you tell us what you actually did? Sure, there is a difference shown. But, you don't say how the difference window was opened. For all I know you are you comparing two versions of the book and one has two hypens, and the the other either an emdash or endash. That sounds reasonable as they are different.
I can take a guess that this is after doing a smarten punctuation in the editor. The other changes seem to agree with this and you vaguely mention it. If so, I don't understand the problem. Two hyphens/dashes together like that should get converted to an emdash. At least, that is what has been done in every punctuation smartener that I have used.
Have I missed the point? If so, please explain in detail what the problem is. And include all the steps needed to reproduce the problem. If you think, "Should I include that detail?", the answer is "yes". And a sample file is always helpful. Maybe a before and after file?
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