We upgraded one of our DC’s to 2008 R2 and everything went fine except for the DNS issue that I blogged about here. After an installation I inspect the server and check to see if everything is ok. I disable hidden en system file viewing in explorer and see what is left. Can across the following two folders $INPLACE.~TR and $WINDOWS.~Q. These folders can be large. In my case they were 3.4 Gig. These folder were left over from the in place upgrade and can be deleted with no consequences.