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The only code I can find in calibre that looks at the attributes of a format file is called when a template referring to a format is evaluated. Are you certain that you don't have a hidden composite column, and in particular a "formats" column? Or perhaps you have installed a plugin that walks through your books?
Copying a library folder will keep many of the preferences, and in particular all the custom columns, hidden or not. There are a large number of preferences stored outside the db.
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