The injection with @EJB should work the same way in a Rest service (CDI Bean) as it does in a Servlet.

@EJB(lookup = "ejb:jboss-ejb-multi-server-app-one/ejb/AppOneBean!org.jboss.as.quickstarts.ejb.multi.server.app.AppOne")
is not working correct if used in a CDI Bean in the reproducer example.

Reproducer can be found here:
git@github.com:wfink/jboss-eap-quickstarts.git
BRANCH: 6.4.x_ejb-multi-server_reproducerEJB-injection
SubProject: ejb-multi-server (used only a part of it to have a web-app and a ejb-app)
see ejb-multi-server/README-reproducerEJB-injection