How do you update a Live drupal server without overwriting the contents?
Thomas Zahreddin is right. But depending on what has changed ("has taken me a couple of weeks ... "), there are more things to consider.


Did you add/change content types. Try to export and import them. Make sure you are not losing contents.
Did you add/change views? You can safely export and import them.
Module Updates. Test them on current data. There's always a chance that user data breaks an update.
Module configuration changes. If it's not too much, take notes and redo them. Else try the features and strong arm modules. Another option is to figure out the exact variable names and write the values into the settings.php.
You have additional content in the dev system. Here things get really hairy. You can try the deployment module or node export. But they are no silver bullets.


If you don't have trivial case, I sugest to test your procedure beforehand. And of course take backups of files and data before you start on the live system. (Backup and Migrate comes in handy here.)