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I've never had an update, either installed through sync or manually, delete any books, fonts, or any files. As a precaution though in case of a reset, I keep a full copy of the reader's contents on my hard drive, and that includes all fonts, books, everything. Then it's a simple matter to just copy everything back to the reader if needed.
My Calibre library is also marked with the 400-500 books that I want to keep on the reader as well. So after a factory reset, or fixing a corrupt database by logging out and back in, or some other hiccup that messes with my content, I can get it all back pretty quickly and painlessly.
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