Well, the way this works is by checking for CityID.apk. If it finds that file, it runs the script to remove the bloat (the packages listed in the first post). If it doesn't find CityID.apk it runs the script that puts the bloatware back.
If you have changed some of the /system apks to .bak (including CityID.apk since that is the "switch") and they are on the list in the first post it should be able to change them back.
If the files you've changed are not on the list, you'll have to manually change them back to .apk