As far as I know, "enderws", canceling a backup will not have any untoward effects, as long as your destination isn't the boot target. We do not modify the source drive in any way...
I've tried to duplicate your problem here, and cannot... I honestly can't think of any reason why copying files from a source, and stopping that copy, would cause any kind of problem unless the destination was selected for startup.
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--Dave Nanian
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