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When a resource is deleted and the BPEL editor is open, it shuts itself down and removes itself from the EMF Model Update Listeners list causing the exception
This was also reported here: https://jira.jboss.org/browse/JBIDE-6785
Fixed in /cvsroot/technology/org.eclipse.bpel/plugins/org.eclipse.bpel.common.ui/src/org/eclipse/bpel/common/ui/editmodel/EditModel.java new revision: 1.6