calibre only deletes old news from within its own library. It never deletes files from readers automatically and it has never done that.
IIRC some models of Kindle have an auto-archive facility that causes old issues of periodicals to be automatically archived. However, that has various caveats and doesn't work very reliably. For example if you send periodicals via email, Amazon auto-converts them to personal docs and they wont auto archive.
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