I think it's not just the problem of sync. If you deploy a module to G server without GEP, it may also produce a "Configuration already exist" exception. I think it's due to the problem of G server deployer. The exception is likely to be thrown in deployment if there has been a deployment happened before and failed. So the best solution for this JIRA is to let G server remove the deployed modules once they're not deployed successfully.
So I suggest to find a scenario always producing the problem and report it to G server as a JIRA. Then, this JIRA can be closed.