CC supports one file, a format, per book. If you send 2 formats for the same book, you see two books in CC. You can send these "extra files" to CC as long as they are recognized as a format and as long as they are enabled in CC's settings, in which case you can sync them from calibre to CC. There is no sync back to calibre. If the file is not a book format (not in CC's list of formats in its settings) then it cannot be sent to CC.
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