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For most people space is not much of an ossue for eBooks as they are so small compared to the size of modern disks so keeping 2 copies is not a big issue.
The alternative is to simply do a "Save to Disk" from calibre to save a copy outside Calibre before doing the Delete in Calibre.
This begs the question - if your only copy of a book is currently in Calibre why are you trying to delete it anyway? Once I have a book in Calibre I personally delete any copies that are NOT in Calibre because I am happy for Calibre to act as the manager for my books (I do back up the Calibre folders for security).
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