I just tested this and I didn't have the problem you described.
Have you been working in debug mode at all? Perhaps you edited the template in the Master Style which cannot be reverted. But you can run the upgrade in place to rebuild the master data which will effectively revert the Master Style.
Did a bit more testing and it only seems to happen on the .css file names. If you goto style properties / general / body / and check the reset button. Update Style Properties. This seems to remove the added code but not reverting the template.