The PDI installer is deleting the .kettle directory on uninstall. This is a new and undesirable behavior.
Tested this issue using the latest pdi installer on 10/21/2012.
After uninstalling PDI the .kettle folder was not deleted and during install only the .spoonrc and kettle.properties file were updated.
This issue is resolved.
Tested this issue using the latest PDI installer and this issue is resolved.