If you are "upgrading" from VaultWiki 3, it's not really just an upgrade. You are basically replacing one add-on with another that happens to have the same name.
You must install VaultWiki 4 side-by-side with your existing VaultWiki 3 add-on and import your VaultWiki 3 data into VaultWiki 4. According to the Readme in the ZIP and
this manual page, you should follow the instructions in this blog in order to import from VaultWiki 3:
https://www.vaultwiki.org/blogs/56/
If you already removed version 3 without following these steps, then you need to restore your database from a backup because you deleted your entire wiki.
You will probably need ticket assistance after the import. It is sometimes hard to tell if you are reading the new wiki or the old wiki, so have one of our staff look at your site before you go ahead and just delete the old version.
If you need a professional install and/or import service, these are available for sale in the Members area, under Services.