I'm not sure what you mean. After you do an upgrade, vb tells you all the templates that you have modified that need to be 'updated'. You can then go edit that template, hit History, and then Compare your current version to the vbulletin default version and see what the differences are. You can then just copy/paste these differences into your template and Save it. I don't think you would want something to do that all 'automatically' because sometimes you will choose to just revert the template and thus delete your chances (for whatever reason).
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