Okay, we keep talking about this so I stopped, just now, opened calibre, and plugged in my kindle. I clicked on the tab at the top to display "Reader" as opposed to "Library." I right-clicked on a book that I had put on my kindle yesterday, non-DRM. The drop-down menu said remove, I said yes, it warned that the book would be "permanently removed from the device." I agreed, and it deleted the book from my Kindle. The book stayed in my calibre library, however. I then turned around and added the book back to my Kindle. So yes, you can delete a book from your Kindle and leave it in your library.
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