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Further note, I've transferred another pair of much more simply formatted epubs to the Kobo app using iTunes. In them the hyperlinks work but there are other strange formatting eccentricities which I won't bother to go into.
I'm beginning to wonder if the problem is really that the app uses the kepub rendering engine for epubs rather than ADE (an app for which has recently appeared in the app store). I tried the kepub rendering engine on my Aura HD a year or so ago and concluded it didn't implement enough of the epub definition to be useful, and, though I don't remember the details, this somewhat reminds me of that.
For now I'm giving up, and going back to iTunes or Marvin. Sorry to waste the time of anyone who started to look into this.
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