Applying global settings for existing users

We have PDFCreator 2.5 to our users w/ the default settings. Recently i have started to look at setting different default settings to speed things up a bit and found how to set them, export the registry and make it the default for new users and that works great. The issue i am having is how to handle users that already have PDFCreator for a while since they already have a HKCU directory for the product and that seems to take precedence over the settings that i am pushing out. We are a virtual desktop environment so it is very easy for me to push out settings/updates to the product but wont affect anything that is in that HKCU hive obviously since the user is not logged in w/ that is pushed. I found i can use a script to just delete that specific registry key but only works if the user is logged in so thought i’d see if anyone had a more efficient way to handle it?