Most places have the developers script their customizations that can be migrated to test and production instances via shell, FNDLOAD and XDOLoader commands. Then when you refresh production back to development, they can just remigrate any customizations that have not been promoted to production yet.
The same requirement exists if you modify a seeded object and a patch from Oracle overwrites your modification. You are responsible for reapplying your modification after any changes.
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Create script to download the Users, responsibilities, workflow changes, functional setups. you can use FNDLOAD, WFLOAD utilities to download these and save it in ldts