@DerekB, is correct. The checkpoint/seek pointers will be honored, but back up your configs as changes don't occur until restart of splunk. Also verify the $SPLUNK_HOME/var/log/splunk/migration.log, this will tell you which files have been modified. What you are mostly concered about is the fishbucket directory.
Here some additional reading: http://docs.splunk.com/Documentation/Splunk/4.3.4/Deploy/Upgradethenixuniversalforwarder http://blogs.splunk.com/2008/08/14/what-is-this-fishbucket-thing/ http://docs.splunk.com/Documentation/Splunk/5.0/Deploy/Deploymentoverview