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Other than yours, I know of no assertion that calibre has *by itself* deleted a book from a library. We *would* hear about it, because calibre has thousands of users and if it was deleting books without permission, it would be considered highly antisocial.
I recognize that it is probably useful to you to make posts like this (makes you feel better, hmmm?). That said, it would be even more useful if you provided some information about the event, such as what was lost and what you were doing. "Everything" is a lot.
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