Like the title says: if a bpel file is deleted from the workspace, the process entry is never removed from the ODE deployment model.
This is part of a bigger problem having to do with refactoring: see https://jira.jboss.org/jira/browse/JBIDE-6018 and https://jira.jboss.org/jira/browse/JBIDE-5027
but at the very least, the deployment model should be kept in sync if bpel files are created or deleted.

Also, if the name of the bpel process is changed, the deployment editor assumes it is a new process and adds it to the model. This is not tragic, but the user must then re-select the inbound and outbound ports.