[Digital Jedi]

When you update vBulletin, your Admin CP will automatically list templates that don't match the current default templates as "out of date". You see, vBulletin kinda just assumes you're running a default skin, or that you haven't made a lot of template edits. It doesn't necessarily know why your templates are different, it just knows they aren't the same as what the new default templates should look like. So it'll warn you that you need to update, so you don't loose any functionality. But if you have a lot of custom style information in those templates, then reverting them is going remove all HTML style changes, which is why your forum will look funny. In cases like that, it's best to go through each template one at a time, compare what the new template should look like verses your existing one and edit them accordingly. Most of the time, if you haven't really found anything needed to be changed, you can just save the template as is, and the message for that one will go away.

Styles are stored in the database, not in files. So you cant retrieve them from an FTP backup. What you can do is simply re-import the skin XML files the same way you did when you first added them.

Also note, when we say you should always make a backup of your forum regularly or before major changes, we mean a database backup. This is where your forum's actual content (posts, profiles, threads, data, passwords, etc.), the meat and potatoes of your site, is actually stored. The files you uploaded via FTP aren't any different than when you first downloaded them from vBulletin.com.