As dwig suggests, it's usually easiest going forward to bring books directly into Calibre, manipulate as required, and then send to the Kindle. But when you're first getting started with Calibre, you might find it best to import/copy your Kindle contents to Calibre and then delete the files off the Kindle. When you've renamed and manipulated the books as you want, you can then copy them back.
Also, just to be clear. Calibre will not, in and of itself, remove the DRM from your books, but will allow you to edit metadata, etc. in Calibre without changing the actual file that is the book. However, if you have the Apprentice Alf plugins installed, then Calibre will unlock your books when you import them.
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