What is the best way to update to a newer version?
You do not have to re-run TV Setup if you uninstall and re-install DVBLink Server. Media Center will pickup your newly re-installed tuners as is with all channels, settings and scheduled recordings.
Since 2.0 the installer will lead you through all the steps necessary. Just run the DVBLink for HDPVR installer and follow the instructions.
You should be able to use your channels in Media Center as they were configured before.