When a wiki is deleted in origin config files, it may happen it is not deleted from the cache files.
I found it is at least the case in the 'deployments' case (when this mechanism is defined in farms.yml). This mode is aiming at delaying the update of a wiki, even if the config files say another version, until the script update.php is run, so that the wiki is not in a inconsistent state since it uses the old version until its database is updated. But the case the wiki is deleted should be anyway taken into account.
To be exhaustive, it should be checked in the various other modes.