The process for this is to remove Atlassian from Google Apps domain side, create a support request at support.atlassian.comfor our team to disable the integration, reintegrate with the new domain. Before you remove the integration please make sure that you have a non google user with admin priveleges to set up the new integration as Google only users may not be able to appropriately login with performing a password reset from the login screen.
Please see the full documentation here: https://confluence.atlassian.com/display/ONDEMANDKB/How+to+Change+Google+Apps+Domain+in+Atlassian+OnDemand+Instances
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