If I were you I would check and find out why it is saying that is 2 seperate folders, Windows does not see folders differently if only the letters case are different. One thing you can do to find out witch one is witch, is set your folder options to warn you if your going into a protected / system directory and the one that comes up with the Warning is the correct windows version, but first off you HAVE to figure out why its saying there is 2 versions
Another thing you can check is see if all of your HDD Space adds up, like maby windows just fucked up and is saying there is 2 folders when in actuality it is one, but is linked some fucked up way. Your HDD space may not be taken up by the second windows directory, even though it is saying it is on the properties, This is how a Multi version of Windows 2000+ CD is made, if you look at the properties of each folder on the CD it is a total of like 3gb, but all it is doing is linking each folder to a different area of the disk (At least that is the only explanation I can see.) ANyway good luck with that :P