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when calibre says you are removing a book from the library, and the book will be deleted, it is absolutely true.
The existence of a backup is entirely irrelevant. For instance, I keep rotating timestamped hardlinked backups of important data via rsync, a common cli alternative to Apple's Time Machine feature -- does that mean if I delete a file the program is lying when it warns me the file is deleted?
Note also, calibre usually deletes to the Recycle Bin anyway.
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