This week's book giveaway is in the Mac OS forum. We're giving away four copies of a choice of "Take Control of Upgrading to Yosemite" or "Take Control of Automating Your Mac" and have Joe Kissell on-line! See this thread for details.
Are the classes in the two JAR files in different packages? Then you can just configure your loggers and appenders in the Log4J configuration file differently for the classes in the two different packages. No need to do complicated tricks.