If JBDS is shutdown whilst a SY project is deployed to a running server, the project disappears from the servers tab but console shows the project is still there when you start the server. This is verified by checking the deployments directory.

Furthermore, you are now unable to right click and add/remove from the server. I tried the same using a standard EAP 6.4.4 install with a WAR and this didn't show the same issues so I guess this is specific to SY tooling?

I'm marking this as a blocker because currently there is no way to recover from this that I can see other than having to recreate the server and projects ALL over again in a different workspace!