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When is JBoss installed with EJB3 configuration, we can't undeploy deployed web module from Netbeans(this feature is disabled). There's JBoss enhancement on this issue ( http://jira.jboss.com/jira/browse/JBINSTALL-44 ) and its implementation should solve this.
Let's wait until the JBoss enhancement is done...then it should start work without any change in NB code. Of course, if JMX management works in the same manner as now.
I can't reproduce this issue neither in 4.0.4 nor in 4.2, thus considering it fixed. If the scenario is still reproducible for you, feel free to reopen the issue. In such a case please attach the exact versions of the jboss, the jdk and the netbeans and steps to reproduce the issue.
VERIFIED