FYI, instead of writing whole post of how to fix the problem, I will redirect you to the correct location so that you know next time where to go;
http://peoplesoft.wikidot.com/message-referenced-in-runtime-tables
http://www.compshack.com/peoplesoft/integration-broker/message-cannot-be-changed-message-referenced-runtime-tables-doc-id-660
Another common integration broker error message we commonly encounter is;
http://peoplesoft.wikidot.com/message-referenced-in-runtime-tables
http://www.compshack.com/peoplesoft/integration-broker/message-cannot-be-changed-message-referenced-runtime-tables-doc-id-660
Another common integration broker error message we commonly encounter is;
Integration Broker: Message Already Used in WSDL
how to fix it is shown in here http://psst0101.digitaleagle.net/2011/10/15/integration-broker-message-already-used-in-wsdl/