Fixed in the current ZIP. Note that this occurs most likely if your wiki did not really experience the problem this upgrade step is attempting to fix.
Download the ZIP again, replace the file vault/install/upgrade_3x300b5.php and run vault/install/upgrade_3x300b5.php?step=2
@we_are_borg, it is normal for the wiki to disappear from the navbar during upgrades. The wiki is automatically disabled to prevent other users from throwing database errors while you are trying to run the upgrade script. The final step of the upgrader will enable it again.