Not really - extract the disc image out of the eboot (or even better start directly from your legal original backup), edit it as desired*, only then convert to eboot
* "reducing quality" isn't something commonly done or trivial to do, if you don't care for videos the usual workaround is to try replacing them with zero-sized files, crosslinking them to a single video and erasing sectors containing the others, or finding extremely short videos in the same format (possibly from some other title)