Why do my em dashes separate into two en dashes only in digital (ebook) format? How do I stop that?

I work for a publisher and we use InDesign to set up our print files to be uploaded (usually in PDF format).
Then I create a new file for the ebooks, removing extra pages, marking the table of content entries as internal hyperlinks, etc.
Since the Kindle Plug-In is still in beta and cannot, for some unknown reason, recognize a TOC created using hyperlinks (even though that is what the instructions specify), I convert to an ePub, check it, do any revisions necessary, save that as the ePub upload.
Then I convert the ePub to mobi using Calibre.
In both instances, my em dashes separate into two en dashes in the digital versions. I use the InDesign Type drop down to select the em dash and it appears as a single symbol or glyph. The print file looks perfect. It is only when it is converted to a digital format that the em dash splits in justified format.
Do I need to find a special glyph to use that is not contained in my font (Times New Roman)? I really need to fix this! Any help is appreciated.

Hi,
Thanks for sharing the files. In the document "OutpassageEbookTextcontent.indd", instead of a em dash, two en dashes are used and probably this is the reason you are seeing them in the EPUB. You can use Find/Change dialog to figure out where these are used. I have sent an email listing down few places where these are used as your files might be confidential and I refrained from posting text snippets on the forum. Please take a look and let me know if I haven't understood your problem correctly.
Regards,
Pooja
InDesign Engineering

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