May I suggest the following, sir:
You take a manual snapshot of your owncloud jail in the storage->snapshots section of the GUI. Having done so, if anything you do in the jail does south, you can snap back to where it is. *THEN*, proceed with the click button upgrade. Then, with the grace of God, you should find your upgrade went fine. If not, you can "revert" your snapshot, and everyone is happy.
What do you think?