Calibre will always use the ORIGINAL_EPUB file when reconverting.
See
Release: 0.8.11 [22 Jul, 2011]
New Features When doing a conversion from some format to the same format, save the original file
When calibre does a conversion from the same format to the same format, for example, from EPUB to EPUB, the original file is saved as original_epub, so that in case the conversion is poor, you can change the settings and run it again. The original is automatically used every time you run a conversion with that format as input. If you want to disable this, there is a tweak that prevents calibre from saving the originals in Preferences->Tweaks. You can easily replace the converted version with the original in the Edit metadata dialog by right clicking on the list of formats in the top right corner.