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@phossler - I run it once a week, before I do my weekly backup.
My libraries are larger (biggest is ~90,000 'books') and probably busier than yours.
I occasionally get errors (rarely more than one or two) in the third stage, but because it must have happened since last week I can always attribute to something outside of calibre - e.g. the video adapter failing, me unzipping a cbz to a subfolder and forgetting to delete the subfolder, the UPS not kicking in on a power fail.
BR
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