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As far as I can tell, that is happening before the device becomes involved. Calibre is making a copy of the book in the temporary storage/directory before updating the metadata, cover or doing any other changes.
That makes me think it is something in the OS that is cause. Usually, it is either space or permissions causing problems like this. But, a time out is strange unless the copy was happening over the network. You need to check where temporary files are created and that you have access and can use it. Beyond that, I don't use a Mac, so can't say for sure.
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