You may be using the wrong directory for your custom files. These should be placed in [tomcat]/shared/classes/alfresco/… If you place them in the expanded [tomcat]webapps/alfresco/… or [tomcat]webapps/share/… then you will lose them when any amp module is installed. See http://docs.alfresco.com/community/tasks/alf-war-install.html Cheers, Sasquatch