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Short answer: back up your Calibre library folder(s), INCLUDING metadata.db. This will back up all the columns in your library, including custom columns.
What this won't protect is some of the settings in the Calibre program itself. For that, you'll also need to back up your configuration folder.
You might also consider using Calibre Portable, even if you have no intention of putting it on a portable drive. Back up all your settings, including your libraries and books, just by backing up your Calibre Portable folder (and all subfolders).
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