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As long as you follow what CRussel posted, once you have Calibre loaded up and your Kindle connected, if you click on "Device" tab/button that appears next to "Library", the screen then shows you what books you have on your Kindle. Delete from that screen and they are deleted from the Kindle, it won't touch the book in your Calibre Library.
Try it out yourself with one book. Delete one from the "Device" and then check to see it's still there when you click the "Library" tab.
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