I have a setup based on geronimo 2.1.3 and I have created another geronimo instance from existing one using the multiple server instance feature.  I had set the following
set GERONIMO_OPTS=-Dorg.apache.geronimo.server.name=instance2 and was able to start another instance with a portOffset of 1.

Later I deployed a WAR application to one of geronimo instance and can see the application in started state in the instance I have deployed the application and stopped
in another instance. I can see an entry in the config.xml as well for both the instances. Another observation in this case is that config.xml for instance2 gets the entry
only when I access the admin console WAR portlet for this instance.

Later tried undeploying the application. Application is removed from the server repository, application entry is removed from config.xml of the instance I have deployed the
application. However the application entry in config.xml of instance2 still remains and is not removed. 

Just tried debugging this issue and found that LocalAttributeManager.java shows the values with relative to g home for example "attributeFile <g_home>\var\config\config.xml".
However it never suggests any value relative to <g_home/instance2>. ServerOverride.java also works out relative to g_home.

Any suggestions on how shall I proceed with this issue will be really helpful.