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It seems like the drop/create should be limited to the the tables being associated by the Hibernate MBean that has the Hbm2ddlAuto flag set.
And which would those be? With HAR deployments you aren't explicitly telling the SessionFacctory which mapping files belong to it; instead the SessionFactory is discovering that for itself from the HAR.
What you are trying *will not* work. In fact, after reading this, I am going to add code to explicitly disallow multiple org.jboss.hibernate.jmx.Hibernate definitions within a single HAR/hibernate-service.xml
These should be two seperate HARs. If you want them to share some resources, bundle them into a SAR.