Could you please provide us with some more info?
What server are you using?
How did you create your project - using JBoss Tools 3.2.0.CR1, any older JBoss Tools version or in any other way?
What do you mean by "mvn-rebuild"?
Could you also please explain the meaning of "when stopping the server while hot-deploying a resource via jboss tools"?
It would be good if you could provide an example of your project.