Does your project include /WEB-INF/web.xml file with context parameter?
<context-param>
<param-name>javax.faces.CONFIG_FILES</param-name>
<param-value>/WEB-INF/second-faces-config.xml</param-value>
</context-param>
File named faces-config.xml is not required to be registered in web.xml, but other named files should be. When you created second-faces-config.xml file by JBoss Tools faces config wizard, it must have added this context parameter so that it was used by content assist. Could it be that later it was removed from web.xml?