I always test an upgrade on a test site first. So I copy over my database from the live site and then upload all the new files there and do an upgrade there and then see if everything works OK. If it does, then I close my live site and upload all the files to there and run the upgrade script.
All the vB settings are stored in the database - except those that point to the database which are in the config.php file. So, if you copy the database to somewhere else (like a test site), one of the first things you need to do is change settings in vboptions > Site Name/URL/etc after you do the upgrade. Also, if avatars/sigpics/attachments are stored in the filesystem, you need to change the path to your new test site.
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