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I make ePubs by hand so I'm not sure what InDesign is doing, but you need to make sure you've done the following:
- Created an iTunesArtwork file (no file extension), which is basically your cover image, which sits in the root of your ePub.
- Created an .html page for your cover image to sit on (and referenced this in the toc.ncx file).
There are things you can do in the content.opf file as well but I wouldn't worry about those until you've done the above.
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