In its current implementation, the JAX-RS core plugin processes annotation changes in the working copies, assuming that they will all be caught (ie, in 'post-change' events). However, in some situations, changing and then saving a compilation unit just after (ie, saving before the 'post-change' event occurs) can lead to sync' issue, where the java model is saved and the jax-rs did not apply the changes.
To avoid such a situation, a 'post-reconcile' processing should be done, too. This processing should do a kind of a 'clean' analyse of the given compilation unit build the associated JAX-RS elements.