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I guess since there has been no response, the answer is this cannot be set or maintained during the upgrade.
I guess the workaround is to add to checklist before to verify and after to change back.
This should be included in some best practice information somewhere (if not already).
Thanks for confirming/re-inforcing this!
Are you stating that the upgrade process is changing or resetting data in DBA_DIRECTORIES ? It should not - if you have documented this experience, pl report it to Support - it may be a known bug or a new one.
The increase in size of the database should only be restricted to SYSTEM and SYSAUX tablespaces (and possibly TEMP and UNDO), but user tablespaces should see no increase.