I first reported this in JBAS-5315, unaware that JBossMetadata project had a separate JIRA.

While debugging one of the issues in a sample application deployed on JBoss-5.0 Beta4, i happened to see the merge(EJBLocalReferenceMetaData override, EJBLocalReferenceMetaData original) method of org.jboss.metadata.javaee.support.MergeableMappedMetaData.EJBLocalReferenceMetaData. There appears to be a typo in this method:

if (override != null && override.local != null)
setLocal(local);

This should have been:

if (override != null && override.local != null)
setLocal(override.local);