Calibre stores metadata in it's own database. There is also metadata in the ebooks. Calibre does not update the metadata in the ebook unless you tell it to. A common way to do this is by doing a conversion. My guess is that you have done this after putting your comments in. The fix for this, other than not pressing that button, is to get calibre to update the metadata in the book again. Another conversion will do this. Also, if you are talking about ePubs, then the Modify ePub plugin will do it as well.
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