,kde and .qt are hidden files written on your first user start of X to save your desktop session i.e. screen resolution icon placement and such. if you upgraded while in X your settings for .kde are not over written with the version because you are still in X --- When doing the upgrade from init3 this is not a problem because you are not in X. there may be a conflict with your now in kde .
\there is no data loss when deleting these files other than your eye candy for the kde desktop. and if you want you can back up these files somewhere else than /home and they can always be put back if this doesn't work --- it's very easy
and last but not least if you did this upgrade while in kde therein lies the problem with X --- when upgrading to Xorg you can not be in a windowed enviroment you must be in init3