This is a problem that has noticed a bit recently with the KoboTouchExtended driver. It is related to how the driver makes the changes to the books. It probably means there are a lot of internal files that need to be change. I will look at changing this when I have time. But, if you are running the 32bit version of calibre, updating to the 64bit version will probably solve it. Or at least push the problem off for a much larger book.
If that doesn't work, you can also try converting the book using the Kepub Output plugin. I won't be surprised if that fails for the same reason as there is a lot of shared code in the extended driver and the output plugin, but, there might be less resource being use elsewhere, so it might work.
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