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The point is that Calibre should not ever be deleting a file from its internal library unless you tell it to. A Send to Device operation make a copy onto your device - the file that is being copied is still inthe calibre library. If you click on a book entry the book formats that are in the calibre library for that book should be listed.
The error message sugges there is no longer any format stored for that book entry. Therefore the question becomes how did the copy in calibre disappear? That was why I wondered if you were deleting the library copy when you thought you were deleting the device copy. Have you checked the calibre book entry to see what format(s) are shown?
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