After the problem with the self check in kwin killing desktop effects and installing the version that didn’t have the self checks the upstream packages were also installed as a “dependency” and after a couple of updates I was able to remove them without YaST freaking out but my themes and window boarders have yet to switch from using the uninstalled upstream themes to the SUSE ones which are installed. I figured if updating caused this then updating will fix it be after installing several updates to KDE 4.1.1 the theme has yet to switch.
“We must plan for freedom, and not only for security, if for no other reason than only freedom can make security more secure.” Karl Popper