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You can also ignore any device even if you told calibre you want to manage it, by simply unplugging it, starting calibre, then going to Preferences->Plugins and customize the MTP plugin, where there is a list of seen devices, which you can choose to ignore.
And note that calibre does not actually scan the entire device, there are a number of "common" folders it skips by default such as Android, Video, Audio, etc.
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