Seif kindly agreed to look into this.

If the DB upgrade cannot be done in-place, I propose to delete or move
it aside when the new version starts. It's better to start with blank DB
after a major upgrade than not starting at all.

Thanks!

** Changed in: zeitgeist (Ubuntu Quantal)
     Assignee: Canonical Desktop Team (canonical-desktop-team) => Seif Lotfy 
(seif)

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https://bugs.launchpad.net/bugs/986928

Title:
  zeitgeist-daemon crashes with "zeitgeist-daemon.vala:473: Unable to
  upgrade from schema version 3"

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