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Sounds like the redeploy is not working, the old EntityManagerFactory is remaining deployed.
What type of app is it, ejb, web, other?
Things should be redeployed correctly for a managed persistence unit (EJB app), as the container undeploys the persistence unit. But for an application managed persistence unit, you are responsible for closing the old EntityManagerFactory, if you don't close it, then the old persistence context will remain.