When using the command line to rebuild a Tuxedo domain, there is a new flag to keep your settings:
–keepfeaturesswitch in the following command was introduced in PeopleTools 8.54.
psadmin –c import [PS_CFG_HOME] –d [old domain name] –n [new domain name] -keepfeatures
This came from the Best Practices guide for Mid-tier Deployment White Paper. At the end of the document, there is a good overview for the steps needed with a PeopleTools upgrade and the commands to help you script the upgrade.