OK, nice to hear that this package installs flawlessly.
The config files and probably the maps are located in your home and will not be removed or overwritten during installation. If you think there is a problem in your config you can remove or rename the dir .opencpn in your home.
To help I need more information about your configuration. Thats why I asked the question which device is configured in opencpn (ToolBox -> GPS -> NMEA
As you wrote about xgps, is there a gpsd installed and running?