So you may need to migrate customMessages.xml to your new 12c environment. Fortunately, there are a few easy steps to achieve this.
1. Take environment backup.
2.Stop all the services
2.Create below folder structure in 12c.
/…/ORACLE_HOME/user_projects/domains/bi/bidata/components/OBIPS/customMessages (for custom xml messaging)
4.Place the customMessages.xml file.
5.Restart the servers.
6.And check the whether you achieved your requirement also.
A sample of my customMessages.xml file: