You could just avoid making them in the first place. See the tweaks within calibre preferences.
Preferences|Advanced|Tweaks.
Quote:
#: Save original file when converting/polishing from same format to same format
# When calibre does a conversion from the same format to the same format, for
# example, from EPUB to EPUB, the original file is saved, so that in case the
# conversion is poor, you can tweak the settings and run it again. By setting
# this to False you can prevent calibre from saving the original file.
# Similarly, by setting save_original_format_when_polishing to False you can
# prevent calibre from saving the original file when polishing.
save_original_format = True
save_original_format_when_polishing = True
|