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I like Davidfor's notion that it might be storage related. One might have a hard time "seeking" or reading from locations just used to store the book and get stuck waiting for data depending on how the drivers for sdhc were written... As long as no other memory locations other than actual file storage were affected there would be no reason to expect trouble with anything else the Kobo is doing.
I'm not saying that is it, but wouldn't a sdhc repair tool allow you to copy the card's contents and format/check disk/repair it? A pain surely, but one more thing you might eliminate. Internal SDHC or external based on where the ebooks were stored and if your model has an internal sdhc.
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