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The upgrade doc instructs the user to compare their COP with the old DEMO db (where all the maintenance fixes had been applied) in order to build a project - UPGCUST - with all the customizations. Later on, in Chapter 4, this UPGCUST project is compared to the 9.1 release flagging all objects that were also modified by Oracle. At this point, an evaluation of which objects will be kept and which will be overridden by the 91 version needs to be taken - step Reviewing New Release Changes. In Chapter 5, step Copying the UPGCUST Project will copy the chosen customizations over to the 9.1 db. When all 9.1 metadata is copied back to your COP, the chosen customizations will be among them.
Hope it helps.