There was an issue https://jira.jboss.org/browse/JBIDE-5974 'Add JSF Capabilities not preserved after restart'. In some cases, for example for projects which could not be converted to Web Dynamic projects, the wizard failed, but still project kept JSF model for the current session; on Eclipse restart, project configuration was resolved as invalid, and jsf nature was removed with a message to log about it 'Project ... has corrupted nature: org.jboss.tools.jsf.jsfnature'. If you have cases of JSF Capabilities 'unexpected' removal, please compare them to the discussion in JBIDE-5974 and report.