Are these 2 jars part of the same application? If yes, then why are the properties files having the same name. Is there any problem in giving two different names to the properties file and using the appropriate one through your code?
The reason i ask these questions is that the properties file is picked by the classloader and if you want to maintain 2 property files with the same name in 2 jars of the *SAME* application, then i dont think thats possible. I believe classloader isolation is possible at application level and not jar level.