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I have had something like this on my Kobo Touch where I modified an epub and made an error on in the xml code. The calibre read was fine with it, but the Kobo Touch didn't show anything from that point on for each file in the epub. But, I haven't seen the result of a conversion leave an error like this. You could try opening it in Sigil to see if it finds any errors.
Another possibility is the colour choose on some styles. If the text isn't simply black and white text, it's possible the Kobo is making it white on white. A quick test for this would be to try and highlight some text on the Kobo by holding you finger where you think there should be some text. If the highlighting menu comes up, you will see how long the word it thinks it found was and either the dictionary lookup or saving an annotation will show what was selected.
Other than that, I can't think of anything. Is there any chance we can get a look at the file to see what it looks like?
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