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The calibre viewer is an EPUB Viewer, it automatically converts non-EPUBs into something it can handle. The images making up a CBR or CBZ are exploded into a directory named xxxxxx-comic-extract (where xxxxxx is a random string, e.g.hrcqpm) within the TEMP directory. When the viewer is closed the xxxxxx-comic-extract folder is deleted.
In which directory are the "extra copies of the .cbr files" being created? And have you redirected calibre's temporary storage location via the CALIBRE_TEMP_DIR environment variable?
BR
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