As for your wiki being vanished, did you hit the Upgrade button after updating to 4.1.1? If not, you need to go into your AdminCP's add-ons list, and to use the controls there to execute the upgrade process.
If there is no upgrade control available, please provide some more information:
- Did you have the VaultWiki add-on disabled AFTER it was upgraded? Is the add-on enabled now? In this case, it is possible for non-admin users to experience a race condition when the navigation entries are not yet disabled even though the add-on is already disabled, leading to their personal navigation cache entering an inconsistent state. I don't think it is possible for this to happen for admin users, because admins bypass the enabled-check. Does the vanishing occur for all users, only non-admins, or certain users including admins?
- If Options > VaultWiki: Site Config > Wiki Active = No, then non-admin users will not be able to access the wiki and may be unable to see navigation entries.