you would need to provide bit more details one how you do that. But in general in case server was restarted while process instance was being executed that will result in transaction rollback and process will remain in the same node as before the last trigger. That means it needs to be retriggered to continue - same way as it was done before. For example if use completed user task and that triggered another node but it failed due to server restart, that would mean user task needs to be completed once again as the state was not persisted.
Timers should survive server restarts and be triggered after server is up and running again.
I use eclipse to stop and start the jboss server, nothing special. I'm working off the Chapter 4. Hello World project which is basically a start node, a business rule, a timer, and a stop node. The only difference between the tutorial and my setup is that I am using an oracle database instead of the H2 database.