When upgrading a Business Connect environment, the new EMS settings do not take effect after deploying the BusinessConnect engines.  These type of errors occurred:
...
caused by: Could not create connection with JMS server.[ Queue Connection Factory = QueueConnectionFactory
User Name = admin
JNDI User Name = admin
JNDI Context URL = tibjmsnaming://tib-ems-XX:99999 
JNDI Context Factory = com.tibco.tibjms.naming.TibjmsInitialContextFactory
]
at com.tibco.plugin.share.jms.impl.JMSUtils.doRecovery(Unknown Source)
at com.tibco.plugin.share.jms.impl.JMSReceiver.for(Unknown Source)
...
>>>

On reviewing, even if in Admin the JNDI URL was "tibjmsnaming://tib-ems-YY:99999", it was pointing to "tibjmsnaming://tib-ems-XX:99999" in the error logs. For some reason, re-deployment of BC wasn't picking up the correct values. Repdeploying the engines had no effect.

During deployment of Business Connect, the files in TIBCO_HOME\tra\domain\<domain_name>\datafiles\BusinessConnect_root need to get updated but it wasnt happening in their environment. The "defaultVars.substvar" file under TIBCO_HOME\tra\domain <domain_name>\datafiles\BusinessConnect_root\defaultVars\gatewayProperties\transports\backoffice\JMS was pointing to the old EMS server.

Update defaultVars.substvar to the correct JNDI context URL

Windows Server 2012 R2

In some cases, the Administrator and Hawk agent may not overwrite the previous deployment.  To resolve the issue, make sure that BusinessConnect is undeployed, and then delete the following directory on all servers with previously deployed BC engines:  $TIBCO_HOME\tra\domain <domain_name>\datafiles\BusinessConnect_root.  Then, deploy and start the engines.