If you want to keep as much information as possible but start with a nice clean set up, export your channels from the set up, uninstall (backup first, you never know!), delete everything left, install, set up everything and import saved data. That will get you back channel list, groups, recordings and scheduled recordings.
That being said I didn't do that
. I uninstalled, cleaned, installed, set up everything, restored all databases and mediaportal.xml (as well as thumbs and webepg config), ran setup again and accepted. I was running one of the latest SVNs so I don't expect that there were many changes. If something goes wrong I can always start from scratch.