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This is the first time I've cancelled a sync, so that couldn't have caused the disk corruption. It was not connected to the computer/Calibre at the time, and it wasn't connected for several minutes. The first time I connected there was no problem, I side loaded the epubs I wanted, ejected the device and no problem.
It's only when I noticed I forgot one and reconnected that I got the message that windows detected a problem with the disk drive (my Kobo device) and asked to scan it.
I didn't get any other errors
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