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@Larry - you set your default conversion preferences using Preferences -> Conversion. That is what writes into those files you found.
Then to make sure that calibre will convert with your latest settings, either on a per book basis make sure you click "Restore default settings" on the conversion dialog. Or select *all* your books, bring up the bulk edit dialog, and tick the checkbox "Remove stored conversion settings for the selected books". This will ensure that if you next do a conversion it will use your default settings not any you might have used on a previous conversion for that book.
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