The easiest solution is to have JDownloader move completed downloads to some specific folder, and then set up a scheduled task via FileBot Node to process all the files in that folder (and move them to another folder) once a day. Please read the Unattended Automation with FileBot Node guide for details and step by step instructions.
Advanced users may prefer to integrate FileBot with JDownloader via Event Scripter directly. You will need basic Linux skills though. See JDownloader Setup for Windows, Linux and Mac OS X for details.