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@babkayaga - you can't mix calibre and non calibre books in the same collection with this plugin. You can have Kindle only collections (that the plugin leaves alone) or Calibre generated collections. You cannot have a Calibre plugin generated collection and "expect" that books that are not in Calibre are going to stay inside it.
So either use two collections, or put all your books in Calibre (the space a book takes up on disk is next to nothing - after all a Kindle only has a limited amount of RAM which your hard-disk will be far greater than).
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