com.ibm.ws.naming.util.InvalidObjectException: Some object reference in the name "MyEJB" relative to the context "path/to/myserver" is invalid.
Some possible causes include a context binding in the name which refers to a destroyed context, or an object binding which contains an invalid EJBHome reference.
[Root exception is org.omg.CORBA.INV_OBJREF: Could not resolve IOR string. vmcid: 0x0 minor code: 0 completed: No]
The lookup of other ejbs in the app is working. The difference is the bean class of this ejb was modified and only the new class file was updated in the ear and the app was updated with this ear file in WAS admin console.
Do I have to regenerate the deployment code(stub/tie etc) for the ejb?
The EJB deployment code only needs to be regenerated if the bean interfaces have been modified or the signature of the bean implementation methods has changed. If those have not changed, then likely the issue is the bean failed to start. Check the logs (Systemout.log and FFDC logs) for any other errors related to that EJB. The application may have started fine, but typically EJB initialization is deferred until first use, which is often the first time the bean is looked up. Finally, verify the logs contain a CNTR0167I message indicating the bean was bound in JNDI using the lookup name.