Scenario to replicate the issue with wso2 esb 4.8.0 create the CAR file by selecting all the proxy services, sequences, endpoints, and local entries. Deploy the car on to WSO2 ESB with console.
This makes deployment of all the artifacts into server.
Now try to un-deploy the car from the console. Except endpoints, local-entries, everything will be un-deployed.
Please let us know the way to resolve this issue without server restart.