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I'm afraid I don't undestand what exactly do you want.
To remove format from Calibre, but have the files in some other folder outside Calibre - just use 'Save to disk' before deleting that format.
Same goes, if you want to delete every trace of the book - save the files to disk and delete the book. Only then Calibre will forget all about it, so what's the point? As theducks said, much easier to use custom columns.
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