JBoss AS 5.0.1.GA does not redeploy new EJB written over old one when EJB JAR does not contain deployment descriptors and EJB is deployed as an exploded folder, not single-file archive.
As discussed in another issue (https://jira.jboss.org/jira/browse/JBIDE-4608), this is because of JBoss AS redeploys EJB if its descriptor is touched. Simple changing .class file is not enough to make JBoss redeploy the EJB, but in the case when there is no deployment descriptor (everything is configured via annotations), nothing may cause redeploy (except full remove and new publish)

Workaround is to have deployment descriptors in the module.