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In my experience Calibre won't deal with ebooks in multiple sub folders, if you try to drag them into the Calibre window they just don't add. So I have all of my ebooks in a single folder.
Once you have them in a single directory you could sort by file type and just highlight the ones you want to import. However, Calibre will handle them all and allow you to convert them to MOBI or the format of your choice if you want. If the books have DRM then you would need to use a Calibre plugin to remove that on convert.
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