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From your description it sound as if you have set the main Dropbox folder as the Calibre library. This is going to make it very difficult to manage your Dropbox space, so you want to tidy things up.
If you use the option within Calibre to move the library to a new folder (create an appropriate empty folder under Dropbox first), then Calibre will move all the files that it believes are part of its library to the new location. What is left behind are files that are candidates for deletion.
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