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Database changes made as part of an upgrade don't seem to be applied, and the generated install manifest looks like it's describing a fresh install instead of an upgrade.

Answer

Check how the install manifest was generated for that build — if the tooling that produces it wasn't run in upgrade mode (or ran against the wrong baseline), it can emit fresh-install-style annotations instead of upgrade deltas, which then causes the actual database changes to be skipped rather than applied; regenerating it correctly for an upgrade context is the fix, not troubleshooting the database changes themselves.

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