Was the ejb module packaged inside the war in the case where you deploy them separately? It's not surprising to get the JNDI name conflict if the same ejb module was deployed twice (once deployed by itself and once as part of the war).
If you want the war to reference the EJBs inside the ejb jar, you should only package the relevant ejb interfaces inside the war instead of trying to adding the whole ejb jar to the war.
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