The JAX-RS metamodel can become out-of-sync with the underlying Java Model. Or at least changes in the metamodel (core) are not revealed at the UI level.

This is the case when:

• a resource was removed out of Eclipse: 'refresh' on the project and 'clean build' don't remove the Endpoint in the 'JAX-RS RESTful Web Services' node in the Project Explorer view
• a new resource was created from Forge (using the 'rest endpoints-from-entity' generation)

Clicking on 'refresh' on the 'JAX-RS RESTful Web Services' node in the Project Explorer view is not a work-around: the list remains in the same state.

—
Do more tests (in race conditions):

• quick changes and then save just after,
• delete the resource,
• recreate with Forge,
• etc..

Look at:

• the Project Explorer view state,
• the validation and the content assist.